Re: [gmx-users] Add missing residue
Hi, There are some suggestions at http://www.gromacs.org/Documentation/File_Formats/Coordinate_File Mark On Sun, Sep 28, 2014 at 4:35 PM, Nizar Masbukhin wrote: > Dear users, > > I'm going to simulate a protein. On the pdb file contents, it's said that > this protein has two chains, and missing residues and atoms. when I try to > pdb2gmx, the error messages occured. It seemed due tue the missing residue > so that i got the message error. > My question is: How can I add missing resiudes and atoms to the pdb files > so that i can use it? > > Thanks > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] How to compute self diffusivities when the xtc trajectory file contains only a subset of atoms
On Sun, Sep 28, 2014 at 5:36 PM, rocwhite168 wrote:
> Hi Mark,
>
> Thanks for your suggestion. That's actually what I've been doing. However,
> it requires modifying not only .top but also conf.gro and grompp.mdp (to
> remove reference to index groups of fixed atoms that no longer exist), as
> well as rerunning make_ndx. I was hoping there would be a less tortuous
> path :)
Sounds like a 10 minute job to me :-) - sed on the gro file, wc -l to check
the number of atoms, text editor to pull out any references in the .mdp
that no longer make sense. You only need the topology definitions in the
.tpr, not anything to do with the physics...
It's strange that .tpr generated by grompp has everything correctly:
>
>moltype (0):
> name="Water"
> atoms:
> atom (4):
> ...
> atom (4):
> atom[0]={name="OW"}
> atom[1]={name="HW"}
> atom[2]={name="HW"}
> atom[3]={name="MW"}
> type (4):
> ...
>
> but .tpr generated by gmx convert-tpr does not:
>
>moltype (0):
> name="This becomes the system name"
> atoms:
> atom (60):
> ...
> atom (60):
> atom[0]={name="OW"}
> atom[1]={name="HW"}
> atom[2]={name="HW"}
> atom[3]={name="MW"}
> atom[4]={name="OW"}
> atom[5]={name="HW"}
> atom[6]={name="HW"}
> atom[7]={name="MW"}
> atom[8]={name="OW"}
> atom[9]={name="HW"}
> atom[10]={name="HW"}
> atom[11]={name="MW"}
> atom[12]={name="OW"}
> ...
>
> Any ideas why this would happen?
>
Like most software, because someone made it work well enough to solve their
immediate problem.
Back on the main question, why aren't you just using index groups on the
trajectory with the tool you were planning to use? That's the simplest time
to take a subset.
Mark
> Thanks,
>
> Roc
>
> On Sun, Sep 28, 2014 at 1:32 AM, Mark Abraham
> wrote:
>
> > Hi,
> >
> > I'm not sure this will help, because I'm not sure what the origin of the
> > problem is, but you can easily hack a copy of your .top so that a fresh
> run
> > of grompp will produce a .tpr that will match the .xtc.
> >
> > Mark
> > On Sep 28, 2014 7:47 AM, "rocwhite168" wrote:
> >
> > > Dear GROMACS users,
> > >
> > > I'm trying to compute mean square displacements for molecules. My
> > > system contains atoms that don't move, so I used "compressed-x-grps"
> > > in grompp.mdp to exclude them from the xtc trajectory file. After
> > > mdrun, I ran "gmx convert-tpr -s topol.tpr -n index.ndx" to reduce the
> > > set of atoms in the tpr file to match those in the xtc file (otherwise
> > > "gmx msd" will fail because the atom indices exceed those found in the
> > > xtc file). Say, for both "compressed-x-grps" and "gmx convert-tpr" I
> > > specified OW_HW to include all water molecules. However, tpxout.tpr
> > > generated by "gmx convert-tpr" treats all water molecules as a large,
> > > single molecule, and as a result "gmx msd" detects only that one
> > > molecule. This would be useful for computing corrected diffusivities,
> > > but is there a way to let "gmx msd" detect individual molecules
> > > correctly if I want to compute self diffusivities?
> > >
> > > Any suggestions would be very much appreciated!
> > >
> > > Thanks,
> > >
> > > Roc
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-requ...@gromacs.org.
> > >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
--
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* Please search the archive at
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Re: [gmx-users] How to compute self diffusivities when the xtc trajectory file contains only a subset of atoms
On Sun, Sep 28, 2014 at 8:32 PM, rocwhite168 wrote:
> On Sun, Sep 28, 2014 at 12:24 PM, Mark Abraham
> wrote:
>
> > On Sun, Sep 28, 2014 at 5:36 PM, rocwhite168
> wrote:
> >
> > > Hi Mark,
> > >
> > > Thanks for your suggestion. That's actually what I've been doing.
> > However,
> > > it requires modifying not only .top but also conf.gro and grompp.mdp
> (to
> > > remove reference to index groups of fixed atoms that no longer exist),
> as
> > > well as rerunning make_ndx. I was hoping there would be a less tortuous
> > > path :)
> >
> >
> > Sounds like a 10 minute job to me :-) - sed on the gro file, wc -l to
> check
> > the number of atoms, text editor to pull out any references in the .mdp
> > that no longer make sense. You only need the topology definitions in the
> > .tpr, not anything to do with the physics...
> >
> > Well, 10 min for one state point, and there are multiple temperatures,
> pressures and mixture compositions ... Not that I'm really going to do this
> manually, but facing the impressive set of auxiliary tools Gromacs has, I
> was hoping that I missed a simpler solution.
At some point in research, you have to do it yourself, because nobody else
has done exactly that. :-) In MD, that often means some kind of script. I
must still be missing something, though, because if all you need is a .tpr
that matches your simulation's compressed-x group, then the .mdp is common
to all such simulation analyses, you already have the input .gro file to
use sed on because you used it for the original grompp, and those and the
.top files are common to all simulations with the same composition.
> It's strange that .tpr generated by grompp has everything correctly:
> > >
> > >moltype (0):
> > > name="Water"
> > > atoms:
> > > atom (4):
> > > ...
> > > atom (4):
> > > atom[0]={name="OW"}
> > > atom[1]={name="HW"}
> > > atom[2]={name="HW"}
> > > atom[3]={name="MW"}
> > > type (4):
> > > ...
> > >
> > > but .tpr generated by gmx convert-tpr does not:
> > >
> > >moltype (0):
> > > name="This becomes the system name"
> > > atoms:
> > > atom (60):
> > > ...
> > > atom (60):
> > > atom[0]={name="OW"}
> > > atom[1]={name="HW"}
> > > atom[2]={name="HW"}
> > > atom[3]={name="MW"}
> > > atom[4]={name="OW"}
> > > atom[5]={name="HW"}
> > > atom[6]={name="HW"}
> > > atom[7]={name="MW"}
> > > atom[8]={name="OW"}
> > > atom[9]={name="HW"}
> > > atom[10]={name="HW"}
> > > atom[11]={name="MW"}
> > > atom[12]={name="OW"}
> > > ...
> > >
> > > Any ideas why this would happen?
> > >
> >
> > Like most software, because someone made it work well enough to solve
> their
> > immediate problem.
> >
> > Back on the main question, why aren't you just using index groups on the
> > trajectory with the tool you were planning to use? That's the simplest
> time
> > to take a subset.
> >
> If I just give the original .tpr and .ndx to "gmx msd", the program will
> crash with a segmentation error because the indices for the atoms in the
> index group I want to analyze are larger than the total number of atoms in
> the .xtc file.
>
... you're using gmx msd -mol?
Mark
> >
> > Mark
> >
> > In any case, thanks for your input.
>
> Roc
>
> >
> > > Thanks,
> > >
> > > Roc
> > >
> > > On Sun, Sep 28, 2014 at 1:32 AM, Mark Abraham <
> mark.j.abra...@gmail.com>
> > > wrote:
> > >
> > > > Hi,
> > > >
> > > > I'm not sure this will help, because I'm not sure what the origin of
> > the
> > > > problem is, but you can easily hack a copy of your .top so that a
> fresh
> > > run
> > > > of grompp will produce a .tpr that will match the .xtc.
> > > >
> > > > Mark
> > > > On Sep 28, 2014 7:47 AM, "rocwhite168" wrote:
Re: [gmx-users] installation and running gromacs on windows
Hi, Did you try http://www.gromacs.org/Documentation/Installation_Instructions#getting-access-to-gromacs-after-installation ? Mark On Mon, Sep 29, 2014 at 9:57 AM, marcello cammarata wrote: > Hi to all. > i had installed gromacs on wondows platform gromacs using cygwin by follow > the advices in the gromacs istallation page. > > When i start the software cygwin, i type cd Gromacs to go inside the > Gromacs forlder, and foward i type > > > pdb2gmx -f namefile.pdb > > i got the message: > > -bash pdb2gmx: command not found > > so, i tryed to follow other advices in some blogs, also to set a path in > the enviroment variables of the computer, but anything was changed. > > > > > > MARCELLO CAMMARATA > Ing., Ph.D., > > 3208790796 > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] g_tune_pme_mpi is not compatible to mdrun_mpi
Hi, It can't be fixed, because there is no surefire way to run an arbitrary tpr on arbitrary number of ranks, regardless of how you guess -npme might succeed. We should just make the check optional, instead of being a deal breaker. Mark On Sep 29, 2014 4:35 PM, "Carsten Kutzner" wrote: > Hi, > > I see where the problem is. > There is an initial check in g_tune_pme to make sure that parallel > runs can be executed at all. This is being run with the automatic > number of PME-only ranks, which is 11 for your input file. > Unfortunately, this results in 37 PP ranks, for which no domain > decomposition can be found. > > At some point in the past we discussed that this could happen > and it should be fixed. Will open a bug entry. > > Thanks, > Carsten > > > On 29 Sep 2014, at 15:36, Ebert Maximilian wrote: > > > Hi, > > > > this ist he command: > > > > setenv MDRUN mdrun_mpi > > > > g_tune_pme_mpi -np 48 -s ../eq_nvt/1ZG4_nvt.tpr -launch > > > > > > Here the output of perf.out > > > > > > > > P E R F O R M A N C E R E S U L T S > > > > > > g_tune_pme_mpi for Gromacs VERSION 5.0.1 > > Number of ranks : 48 > > The mpirun command is : mpirun > > Passing # of ranks via : -np > > The mdrun command is : mdrun_mpi > > mdrun args benchmarks : -resetstep 100 -o bench.trr -x bench.xtc -cpo > bench.cpt -c bench.gro -e bench.edr -g bench.log > > Benchmark steps : 1000 > > dlb equilibration steps : 100 > > mdrun args at launchtime: > > Repeats for each test : 2 > > Input file : ../eq_nvt/1ZG4_nvt.tpr > > PME/PP load estimate : 0.151964 > > Number of particles : 39489 > > Coulomb type : PME > > Grid spacing x y z : 0.114561 0.114561 0.114561 > > Van der Waals type : Cut-off > > > > Will try these real/reciprocal workload settings: > > No. scaling rcoulomb nkx nky nkz spacing rvdw tpr file > > 0 1.00 1.20 72 72 72 0.12 1.20 > ../eq_nvt/1ZG4_nvt_bench00.tpr > > 1 1.10 1.32 64 64 64 0.132000 1.32 > ../eq_nvt/1ZG4_nvt_bench01.tpr > > 2 1.20 1.44 60 60 60 0.144000 1.44 > ../eq_nvt/1ZG4_nvt_bench02.tpr > > > > Note that in addition to the Coulomb radius and the Fourier grid > > other input settings were also changed (see table above). > > Please check if the modified settings are appropriate. > > > > Individual timings for input file 0 (../eq_nvt/1ZG4_nvt_bench00.tpr): > > PME ranks Gcycles ns/dayPME/fRemark > > > > > > Cannot run the benchmark simulations! Please check the error message of > > mdrun for the source of the problem. Did you provide a command line > > argument that neither g_tune_pme nor mdrun understands? Offending > command: > > > > mpirun -np 48 mdrun_mpi -npme 11 -s ../eq_nvt/1ZG4_nvt_bench00.tpr > -resetstep 100 -o bench.trr -x bench.xtc -cpo bench.cpt -c bench.gro -e > bench.edr -g bench.log -nsteps 1 -quiet > > > > > > > > and here are parts of the bench.log: > > > > Log file opened on Mon Sep 29 08:56:38 2014 > > Host: node-e1-67 pid: 24470 rank ID: 0 number of ranks: 48 > > GROMACS:gmx mdrun, VERSION 5.0.1 > > > > GROMACS is written by: > > Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar > > Aldert van Buuren Rudi van DrunenAnton Feenstra Sebastian > Fritsch > > Gerrit GroenhofChristoph Junghans Peter Kasson Carsten Kutzner > > Per LarssonJustin A. Lemkul Magnus LundborgPieter > Meulenhoff > > Erik Marklund Teemu Murtola Szilard Pall Sander Pronk > > Roland Schulz Alexey ShvetsovMichael Shirts Alfons Sijbers > > Peter Tieleman Christian Wennberg Maarten Wolf > > and the project leaders: > > Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel > > > > Copyright (c) 1991-2000, University of Groningen, The Netherlands. > > Copyright (c) 2001-2014, The GROMACS development team at > > Uppsala University, Stockholm University and > > the Royal Institute of Technology, Sweden. > > check out http://www.gromacs.org for more information. > > > > GROMACS is free software; you can redistribute it and/or modify it > > under the terms of the GNU Lesser General Public License
Re: [gmx-users] g_tune_pme_mpi is not compatible to mdrun_mpi
Hi, That seems suitable. Mark On Mon, Sep 29, 2014 at 6:32 PM, Carsten Kutzner wrote: > Hi, > > On 29 Sep 2014, at 18:17, Mark Abraham wrote: > > > Hi, > > > > It can't be fixed, because there is no surefire way to run an arbitrary > tpr > > on arbitrary number of ranks, regardless of how you guess -npme might > > succeed. > What about making this check on two ranks always, regardless of > what was specified on the g_tune_pme command line? On two ranks, > we will never have separate PME ranks, so it should always work, > since we end up with two ranks, doing PP and then PME. > If the system is so small that you can not decompose it in two > DD domains, there is no use to do tuning anyway. > > So even if you say > g_tune_pme -np 48 -s input.tpr > > we first check with > mpirun -np 2 mdrun -s input.tpr > > and only after that continue with -np 48. > > Carsten > > > We should just make the check optional, instead of being a deal > > breaker. > > > > Mark > > On Sep 29, 2014 4:35 PM, "Carsten Kutzner" wrote: > > > >> Hi, > >> > >> I see where the problem is. > >> There is an initial check in g_tune_pme to make sure that parallel > >> runs can be executed at all. This is being run with the automatic > >> number of PME-only ranks, which is 11 for your input file. > >> Unfortunately, this results in 37 PP ranks, for which no domain > >> decomposition can be found. > >> > >> At some point in the past we discussed that this could happen > >> and it should be fixed. Will open a bug entry. > >> > >> Thanks, > >> Carsten > >> > >> > >> On 29 Sep 2014, at 15:36, Ebert Maximilian > wrote: > >> > >>> Hi, > >>> > >>> this ist he command: > >>> > >>> setenv MDRUN mdrun_mpi > >>> > >>> g_tune_pme_mpi -np 48 -s ../eq_nvt/1ZG4_nvt.tpr -launch > >>> > >>> > >>> Here the output of perf.out > >>> > >>> > >>> > >>> P E R F O R M A N C E R E S U L T S > >>> > >>> > >>> g_tune_pme_mpi for Gromacs VERSION 5.0.1 > >>> Number of ranks : 48 > >>> The mpirun command is : mpirun > >>> Passing # of ranks via : -np > >>> The mdrun command is : mdrun_mpi > >>> mdrun args benchmarks : -resetstep 100 -o bench.trr -x bench.xtc -cpo > >> bench.cpt -c bench.gro -e bench.edr -g bench.log > >>> Benchmark steps : 1000 > >>> dlb equilibration steps : 100 > >>> mdrun args at launchtime: > >>> Repeats for each test : 2 > >>> Input file : ../eq_nvt/1ZG4_nvt.tpr > >>> PME/PP load estimate : 0.151964 > >>> Number of particles : 39489 > >>> Coulomb type : PME > >>> Grid spacing x y z : 0.114561 0.114561 0.114561 > >>> Van der Waals type : Cut-off > >>> > >>> Will try these real/reciprocal workload settings: > >>> No. scaling rcoulomb nkx nky nkz spacing rvdw tpr file > >>> 0 1.00 1.20 72 72 72 0.12 1.20 > >> ../eq_nvt/1ZG4_nvt_bench00.tpr > >>> 1 1.10 1.32 64 64 64 0.132000 1.32 > >> ../eq_nvt/1ZG4_nvt_bench01.tpr > >>> 2 1.20 1.44 60 60 60 0.144000 1.44 > >> ../eq_nvt/1ZG4_nvt_bench02.tpr > >>> > >>> Note that in addition to the Coulomb radius and the Fourier grid > >>> other input settings were also changed (see table above). > >>> Please check if the modified settings are appropriate. > >>> > >>> Individual timings for input file 0 (../eq_nvt/1ZG4_nvt_bench00.tpr): > >>> PME ranks Gcycles ns/dayPME/fRemark > >>> > >>> > >>> Cannot run the benchmark simulations! Please check the error message of > >>> mdrun for the source of the problem. Did you provide a command line > >>> argument that neither g_tune_pme nor mdrun understands? Offending > >> command: > >>> > >>> mpirun -np 48 mdrun_mpi -npme 11 -s ../eq_nvt/1ZG4_nvt_bench00.tpr > >> -resetstep 100 -o bench.trr -x bench.xtc -cpo bench.cpt -c bench.gro -e > >> b
Re: [gmx-users] g_tune_pme and verlet
IIRC this was fixed in 4.6.6 (check release notes). You can use a more recent g_tune_pme with older mdrun, in this case. Mark On Sep 29, 2014 7:47 PM, "Åke Sandgren" wrote: > On 09/29/2014 07:17 PM, Carsten Kutzner wrote: > >> >> On 29 Sep 2014, at 19:10, Åke Sandgren wrote: >> >> Hi! >>> >>> I'm trying to run g_tune_pme on a case with verlet lists, but i get >>> complaints from mdrun that >>> “With Verlet lists rcoulomb and rvdw should be identical” >>> >> But does mdrun like your input file? >> > > Yes, it only fails when rcoulomb is changed. I.e. the first sequence of > tests is ok. > > -- > Ake Sandgren, HPC2N, Umea University, S-90187 Umea, Sweden > Internet: a...@hpc2n.umu.se Phone: +46 90 7866134 Fax: +46 90-580 14 > Mobile: +46 70 7716134 WWW: http://www.hpc2n.umu.se > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Problems installing Gromacs 5.0.1
Hi, Spelling download with only one 'a' could help :-) Mark On Tue, Sep 30, 2014 at 4:16 PM, Claudia Fernandes < cs.fernandes0...@gmail.com> wrote: > Hello everyone! > I tried to install Gromacs 5.0.1. > > After this command: > > cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON > > (as described in the gromacs installation information) > > It tries to download of the regressiontest pack from the internet which is > no longer available. > I tried to turn the option off and give it the path to another set of > regression tests (as > > cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNALOAD=OFF > -DREGRESSIONTEST_PATH=/home/user/gromacs-5.0.1/build/regressiontests) > > but it still tries to download the file with no success. > > Any ideas? > > Thank you > Cláudia Fernandes > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] performance 1 gpu
Hi, Not really surprising. The compiler teams try to optimize the performance of lots of different kinds of code on a range of platforms. Some kinds of code aren't prioritized for a given compiler team. Often there are trade-offs that mean some kinds of code gets faster while others get slower, perhaps differently for different hardware targets, while everybody gradually tries to reach nirvana. Actual performance is a matter of how well a specific code works with a specific compiler on specific hardware. Mark On Wed, Oct 1, 2014 at 2:24 PM, Johnny Lu wrote: > That is surprising. I thought intel compiler is the best compiler for intel > cpu. > > On Tue, Sep 30, 2014 at 5:40 PM, Szilárd Páll > wrote: > > > Unfortunately this is an ill-balanced hardware setup (for GROMACS), so > > what you see is not unexpected. > > > > There are a couple of things you can try, but don't expect more than a > > few % improvement: > > - try to lower nstlist (unless you already get a close to 0 buffer); > > this will decrease the non-bonded time, hence the CPU waiting/idling, > > but it will also increase the search time (and DD time if applicable), > > so you'll have to see what wors best for you; > > - try to use the -nb gpu_cpu mode, this does a rather splitting the > > non-bonded workload, but if you are lucky (=you don't get too much > > non-local load which will be computed now on the CPU), you may be able > > to get a bit better performance. > > > > You may want to try gcc 4.8 or 4.9 and FFTW 3.3.x, you will most > > likely get better performance than with icc+MKL. > > > > > > On Thu, Sep 25, 2014 at 12:50 PM, Johnny Lu > > wrote: > > > Hi. > > > > > > I wonder if gromacs 4.6.7 can run faster on xsede.org because I see > cpu > > > waits for gpu in the log. > > > > > > There is 16 cpu (2.7 GHz), 1 phi co-processor, and 1 GPU. > > > > Get that Phi swapped to a GPU and you'll be happier ;) > > > > > I compiled gromacs with gpu and without phi and with intel compiler and > > mkl. > > > > > > I didn't install for 5.0.1 because I worry this bug might mess up > > > equilibration when I switch from one ensemble to another one ( > > > http://redmine.gromacs.org/issues/1603). > > > > It's been fixed, 5.0.2 will be released soon, so I suggest you wait for > it. > > > > > Below are from the log: > > > > > > Gromacs version:VERSION 4.6.7 > > > Precision: single > > > Memory model: 64 bit > > > MPI library:thread_mpi > > > OpenMP support: enabled > > > GPU support:enabled > > > invsqrt routine:gmx_software_invsqrt(x) > > > CPU acceleration: AVX_256 > > > FFT library:MKL > > > Large file support: enabled > > > RDTSCP usage: enabled > > > Built on: Wed Sep 24 08:33:22 CDT 2014 > > > Built by: jlu...@login2.stampede.tacc.utexas.edu [CMAKE] > > > Build OS/arch: Linux 2.6.32-431.17.1.el6.x86_64 x86_64 > > > Build CPU vendor: GenuineIntel > > > Build CPU brand:Intel(R) Xeon(R) CPU E5-2680 0 @ 2.70GHz > > > Build CPU family: 6 Model: 45 Stepping: 7 > > > Build CPU features: aes apic avx clfsh cmov cx8 cx16 htt lahf_lm mmx > msr > > > nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 > sse4.1 > > > sse4.2 ssse3 tdt x2apic > > > C compiler: > > > /opt/apps/intel/13/composer_xe_2013.3.163/bin/intel64/icc Intel icc > (ICC) > > > 13.1.1 20130313 > > > C compiler flags: -mavx-mkl=sequential -std=gnu99 -Wall -ip > > > -funroll-all-loops -O3 -DNDEBUG > > > C++ compiler: > > > /opt/apps/intel/13/composer_xe_2013.3.163/bin/intel64/icc Intel icc > (ICC) > > > 13.1.1 20130313 > > > C++ compiler flags: -mavx -Wall -ip -funroll-all-loops -O3 > -DNDEBUG > > > Linked with Intel MKL version 11.0.3. > > > CUDA compiler: /opt/apps/cuda/6.0/bin/nvcc nvcc: NVIDIA (R) Cuda > > > compiler driver;Copyright (c) 2005-2013 NVIDIA Corporation;Built on > > > Thu_Mar_13_11:58:58_PDT_2014;Cuda compilation tools, release 6.0, > V6.0.1 > > > CUDA compiler > > > > > > flags:-gencode;arch=compute_20,code=sm_20;-gencode;arch=compute_20,code=sm_21;-gencode;arch=compute_30,code=sm_30;-gencode;arch=compute_35,code=sm_35;-gencode;arch=compute_35,code=compute_35;-use_fast_math;; > > > -mavx;-Wall;-ip;-funroll-all-loops;-O3;-DNDEBUG > > > CUDA driver:6.0 > > > CUDA runtime: 6.0 > > > > > > ... > > > Using 1 MPI thread > > > Using 16 OpenMP threads > > > > > > Detecting CPU-specific acceleration. > > > Present hardware specification: > > > Vendor: GenuineIntel > > > Brand: Intel(R) Xeon(R) CPU E5-2680 0 @ 2.70GHz > > > Family: 6 Model: 45 Stepping: 7 > > > Features: aes apic avx clfsh cmov cx8 cx16 htt lahf_lm mmx msr > > nonstop_tsc > > > pcid pclmuldq pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 > > ssse3 > > > tdt x2apic > > > Acceleration most likely to fit this hardware: AVX_256 > > > Acceleration selected at GROMACS compile time: AVX_256 > > > > > > > > > 1 GPU detected: > > > #0: NVIDIA Tesla K20m, compute cap.
[gmx-users] Gromacs 5.0.2 released
Hi Gromacs users, The official release of Gromacs 5.0.2 is available! It contains a fix for a major simulation correctness problem with PME + GPUs in 5.0 and 5.0.1. Please see the link to the release notes below for more details. There are also some other minor bug fixes and performance enhancements. We encourage all users to upgrade their installations from earlier 5.0 releases, particularly for use on GPUs. You can find the code, manual, release notes, installation instructions and test suite at the links below. ftp://ftp.gromacs.org/pub/gromacs/gromacs-5.0.2.tar.gz ftp://ftp.gromacs.org/pub/manual/manual-5.0.2.pdf http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_5.0.x#Release_notes_for_5.0.2 http://www.gromacs.org/Documentation/Installation_Instructions_for_5.0 http://gerrit.gromacs.org/download/regressiontests-5.0.2.tar.gz Happy simulating! Mark Abraham Gromacs development manager -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] User tabulated potentials with cutoff-scheme = verlet, GROMACS 5.0.1 and 5.0.2
On Thu, Oct 2, 2014 at 11:58 AM, Francesco Mambretti < francesco.mambre...@studenti.unimi.it> wrote: > Dear all, I am a student in Physics at Milan University. For my thesis, I > should run a simulation of a binary liquid mixture of Argon and Krypton. > > Until now, I have been learning how to use GROMACS (version 5.0.1 and, > since > yesterady, 5.0.2) essentials, and my simulations were all based on LJ > potential, and all was fine. > > Now I want to use a tabulated potential, that is a more detailed potential, > different in form from LJ, taken from literature. > I followed the steps of the instructions on GROMACS website > ( > http://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials?highlight=tabulated+potential > ) > and the attached pdf, but it doesn't work. > I ought to use cutoff-scheme = verlet (because the "group" scheme does not > make sense, because my system has no charge), VDW-only systems work fine in the group scheme, e.g. with a single atom per charge group - but you will need to organize your own details for adequate buffering. > but I receive these errors > from grompp: > > ERROR 1 [file Aziz.mdp]: > With Verlet lists only cut-off and PME LJ interactions are supported > > > ERROR 2 [file Aziz.mdp]: > With Verlet lists only cut-off, reaction-field, PME and Ewald > electrostatics are supported > > Aziz.mdp is my mdp file, that contains the instructions coulombtype = User > and vdwtype = User. > > What am I missing? > Or it is true that GROMACS is not able to use user-defined potentials with > verlet's cutoff? This would be a serious handicap for this code! > Am I forced to use charge groups? > For now, yes. There is work in progress to implement user tables for the Verlet scheme (& GPUs). Some help with alpha-stage testing would be very welcome! But for that, you might like to have a working group-scheme setup against which to validate. Mark > Thanks in advance, > > Francesco Mambretti - University of Milan - LCP (Parallel Computing Lab) > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] g_tune_pme_mpi is not compatible to mdrun_mpi
Hi, Please note that gmx tune_pme -nocheck is available in 5.0.2 to circumvent this check. Mark -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] R: Re: User tabulated potentials with cutoff-scheme = verlet, GROMACS 5.0.1 and 5.0.2
On Thu, Oct 2, 2014 at 1:13 PM, Francesco Mambretti < francesco.mambre...@studenti.unimi.it> wrote: > So then, you have to update the pages on your website ( > http://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials?highlight=tabulated+potential) > about tabulated potentials, Indeed, I have fixed that. Unfortunately, much of the Gromacs documentation precedes the existence of the Verlet scheme, and we have not made a systematic attempt to update all of it. > and also in the user manual (5.0.1 version). > Noted > Otherwise, people risks misleading about this topic! > In fact, I spent my last month in learning GROMACS, encouraged by the > documentation about tabulated potentials (it seems so easy to do that!), > and nothing is said about the cutoff scheme you have to use! And also the > attached pdf should be updated. > That would be up to the user who contributed it, unfortunately. This is a very strong limit, LJ and Buckingham potentials are often not so > accurate potentials, if you really want to simulate physical systems. > > So the alternatives I have are: > 1) use group charge (e.g.: I have 108 atoms of mixed Ar and Kr, and each > of them is a group charge) and group cutoff - but the run will require more > time > I'd expect that a tiny VDW-only system like that will show little to no performance difference between the cutoff schemes (assuming the group scheme setup is buffered), because both make about the same use of SIMD intrinsics and the effect spent in optimizing for your kind of systems is about the same in both. Once tables work in Verlet, I'd expect even less difference between the two (but GPU support will be great for larger systems). 2) downgrade my GROMACS version, so that I am not forced to use verlet > cutoff if I want a configuration that scales fast > You're not forced to use Verlet now ;-) The default scheme changed in 5, but the group scheme is still there (and works better than ever). There's zero value in using an earlier version. Mark 3) use LJ potential > > Am I right? > > Francesco > > Il 02/10/14, Mark Abraham ha scritto: > > On Thu, Oct 2, 2014 at 11:58 AM, Francesco Mambretti < > > francesco.mambre...@studenti.unimi.it> wrote: > > > > > Dear all, I am a student in Physics at Milan University. For my > thesis, I > > > should run a simulation of a binary liquid mixture of Argon and > Krypton. > > > > > > Until now, I have been learning how to use GROMACS (version 5.0.1 and, > > > since > > > yesterady, 5.0.2) essentials, and my simulations were all based on LJ > > > potential, and all was fine. > > > > > > Now I want to use a tabulated potential, that is a more detailed > potential, > > > different in form from LJ, taken from literature. > > > I followed the steps of the instructions on GROMACS website > > > ( > > > > http://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials?highlight=tabulated+potential > > > ) > > > and the attached pdf, but it doesn't work. > > > I ought to use cutoff-scheme = verlet (because the "group" scheme does > not > > > make sense, because my system has no charge), > > > > > > VDW-only systems work fine in the group scheme, e.g. with a single atom > per > > charge group - but you will need to organize your own details for > adequate > > buffering. > > > > > > > but I receive these errors > > > from grompp: > > > > > > ERROR 1 [file Aziz.mdp]: > > > With Verlet lists only cut-off and PME LJ interactions are supported > > > > > > > > > ERROR 2 [file Aziz.mdp]: > > > With Verlet lists only cut-off, reaction-field, PME and Ewald > > > electrostatics are supported > > > > > > Aziz.mdp is my mdp file, that contains the instructions coulombtype = > User > > > and vdwtype = User. > > > > > > What am I missing? > > > Or it is true that GROMACS is not able to use user-defined potentials > with > > > verlet's cutoff? This would be a serious handicap for this code! > > > Am I forced to use charge groups? > > > > > > > For now, yes. There is work in progress to implement user tables for the > > Verlet scheme (& GPUs). Some help with alpha-stage testing would be very > > welcome! But for that, you might like to have a working group-scheme > setup > > against which to validate. > > > > Mark > > > > > > > Thanks in advance, > > > > > > Francesco Mambretti - University of Milan - LCP (Parallel Computing &g
Re: [gmx-users] R: Re: R: Re: User tabulated potentials with cutoff-scheme = verlet, GROMACS 5.0.1 and 5.0.2
On Thu, Oct 2, 2014 at 3:24 PM, Francesco Mambretti < francesco.mambre...@studenti.unimi.it> wrote: > Ok thank you. Another question. 108 particles was just a test for > beginning, but we would like to study much bigger systems (from 1000 to > 1 particles at least). Is it possible and reasonable with the group > scheme? Does it support parallel computing? > Sure, for the last 15 years. :-) The group scheme has only MPI support (no OpenMP, no CUDA), so in practice you're limited to something like at least 500 atoms per rank(=core). YMMV because we don't study the performance on such systems. Mark > Francesco > > Il 02/10/14 13:43, Mark Abraham ha scritto: > > > > On Thu, Oct 2, 2014 at 1:13 PM, Francesco Mambretti < > > francesco.mambre...@studenti.unimi.it> wrote: > > > > > So then, you have to update the pages on your website ( > > > > http://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials?highlight=tabulated+potential > ) > > > about tabulated potentials, > > > > > > Indeed, I have fixed that. Unfortunately, much of the Gromacs > documentation > > precedes the existence of the Verlet scheme, and we have not made a > > systematic attempt to update all of it. > > > > > > > and also in the user manual (5.0.1 version). > > > > > > > Noted > > > > > > > Otherwise, people risks misleading about this topic! > > > In fact, I spent my last month in learning GROMACS, encouraged by the > > > documentation about tabulated potentials (it seems so easy to do > that!), > > > and nothing is said about the cutoff scheme you have to use! And also > the > > > attached pdf should be updated. > > > > > > > That would be up to the user who contributed it, unfortunately. > > > > This is a very strong limit, LJ and Buckingham potentials are often not > so > > > accurate potentials, if you really want to simulate physical systems. > > > > > > So the alternatives I have are: > > > 1) use group charge (e.g.: I have 108 atoms of mixed Ar and Kr, and > each > > > of them is a group charge) and group cutoff - but the run will require > more > > > time > > > > > > > I'd expect that a tiny VDW-only system like that will show little to no > > performance difference between the cutoff schemes (assuming the group > > scheme setup is buffered), because both make about the same use of SIMD > > intrinsics and the effect spent in optimizing for your kind of systems is > > about the same in both. Once tables work in Verlet, I'd expect even less > > difference between the two (but GPU support will be great for larger > > systems). > > > > 2) downgrade my GROMACS version, so that I am not forced to use verlet > > > cutoff if I want a configuration that > > > > scales fast > > > > > > > You're not forced to use Verlet now ;-) The default scheme changed in 5, > > but the group scheme is still there (and works better than ever). There's > > zero value in using an earlier version. > > > > Mark > > > > 3) use LJ potential > > > > > > Am I right? > > > > > > Francesco > > > > > > Il 02/10/14, Mark Abraham ha scritto: > > > > On Thu, Oct 2, 2014 at 11:58 AM, Francesco Mambretti < > > > > francesco.mambre...@studenti.unimi.it> wrote: > > > > > > > > > Dear all, I am a student in Physics at Milan University. For my > > > thesis, I > > > > > should run a simulation of a binary liquid mixture of Argon and > > > Krypton. > > > > > > > > > > Until now, I have been learning how to use GROMACS (version 5.0.1 > and, > > > > > since > > > > > yesterady, 5.0.2) essentials, and my simulations were all based on > LJ > > > > > potential, and all was fine. > > > > > > > > > > Now I want to use a tabulated potential, that is a more detailed > > > potential, > > > > > different in form from LJ, taken from literature. > > > > > I followed the steps of the instructions on GROMACS website > > > > > ( > > > > > > > > > http://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials?highlight=tabulated+potential > > > > > ) > > > > > and the attached pdf, but it doesn't work. > > > > > I ought to use cutoff-scheme = verlet (because the "group" scheme > does
Re: [gmx-users] Invalid order for directive bondtypes
You probably need to define [atomtypes] before you can define [bondtypes] that use them. So swap the order of your #include statements. Mark On Mon, Oct 6, 2014 at 6:18 AM, Atila Petrosian wrote: > Dear gromacs users > > I want to do MD simulation of a CNT. > > I used aromatic carbon from charmm.ff > > I created a cnt.ff folder containing following files: > > ffcnt.atp: > --- > CA12.01100 ;aromatic C > - > ffcnt.n2t: > --- > CCA0.00 12.0113C 0.141 C 0.141 C 0.141 > CCA0.00 12.0112C 0.141 C 0.141 > - > ffcntbonded.itp: > > [ bondtypes ] > ; i j func b0 kb > CA CA10.1375 0.0 > > [ angletypes ] > ; i j k func th0 cth ub0 cub > CA CA CA 5 120.00 0.0 0.24162 29288.0 > > [ dihedraltypes ] > ; i j k l funcphi0cp mult > CA CA CA CA 9 180.00 0.0 2 > - > ffcntnonbonded.itp: > - > [ atomtypes > ] > ;nameat.nummasschargeptypesigma > epsi > CA 612.011000.00A 0.335 > 0.234463 > - > ffcnt.rtp: > -- > [ bondedtypes > ] > ; Col 1: Type of > bond > ; Col 2: Type of > angles > ; Col 3: Type of proper > dihedrals > ; Col 4: Type of improper > dihedrals > ; Col 5: Generate all dihedrals if 1, only heavy atoms of > 0. > ; Col 6: Number of excluded neighbors for nonbonded > interactions > ; Col 7: Generate 1,4 interactions between pairs of hydrogens if > 1 > ; Col 8: Remove propers over the same bond as an improper if it is > 1 > ; bonds angles dihedrals impropers all_dihedrals nrexcl HH14 > RemoveDih > 1 5 921 3 1 > 0 > > > [ ALA > ] > [ atoms > ] > NNH1-0.47 > 0 > HNH0.31 > 1 > CACT10.07 > 2 > HAHB0.09 > 3 > CBCT3-0.27 > 4 > HB1HA0.09 > 5 > HB2HA0.09 > 6 > HB3HA0.09 > 7 > CC0.51 > 8 > OO-0.51 > 9 > . > . > . > - > forcefield.itp: > > #define _FF_CNT > > [ defaults ] > ; nbfunccomb-rulegen-pairsfudgeLJfudgeQQ > 1 2 yes 1.01.0 > > #include "ffcntbonded.itp" > #include "ffcntnonbonded.itp" > - > > After creating cnt.top file using g_x2top, I used grompp for energy > minimization, but I encountered with Fatal Error: > > Syntax error - File ffcntbonded.itp, line 1 > Last line read: > '[ bondtypes ]' > Invalid order for directive bondtypes > > Before doing MD simulation, I checked carbon nanotube in the GROMACS > website: > > > http://www.gromacs.org/Documentation/How-tos/Carbon_Nanotube?highlight=nanotube > > In my opinion, my manner is true. > > How to solve this problem? > > Any help will highly appreciated. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Invalid order for directive bondtypes
On Oct 6, 2014 3:57 PM, "Atila Petrosian" wrote: > > Dear Mark > > Very thanks for you reply. > > I solved previous problem by swapping the order of my #include statements > in forcefield.itp file. > > I used grompp for energy minimization, I obtained em.tpr file without any > problem. Then I used mdrun for energy minimization, this step was done > without error, but, when I see gro file obtained from minimization using > VMD, there is unusual state. Those figures related to this state are in > following links: > > https://www.dropbox.com/s/ofyknhton3cmelp/figure.TIF?dl=0 > > https://www.dropbox.com/s/g71xgjolka9x0v4/figureII.TIF?dl=0 > > What is the reason of this state? No connectivity is present in a .gro file. How is VMD supposed to present information that isn't there? It guesses, assuming the file contains a protein, as discussed in every second post here that concerns VMD. Your .top file is definitive. Google will show a few tools that might help here. > How to solve this problem? Understand what your tools do! :-) Mark > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] can not split pdb beyond 1019
Hi, Thanks, good report. Unfortunately, someone in prehistoric times implemented the functionality common to -sep and -split using the or operator... everywhere except closing the file. So -split will continue opening files until it runs out of file handles (so later on, files can't be opened), and maybe accidentally write something to disk, depending how the OS works. I've uploaded a fix for a future 5.0.x version. Mark On Mon, Oct 6, 2014 at 4:18 PM, gromacs query wrote: > Hi All, > > I am trying to split my trajectory in single frame pdbs for some analysis > using trjconv but it ends with an error after ouput 1019 pdbs. I tried with > different version of gromacs (4.6.3 and 5.0) its the same error. > > trjconv -s ../em.tpr -f ../image_fitted.trr -o test.pdb -split 10 -b 4 > -e 96000 -n ndx.ndx > > > error > > /src/gmxlib/futil.c, line: 1032 > > Fatal error: > Library file residuetypes.dat not found in current dir nor in default > directories. > > > Why 1019 is a magic number? Even I tried changing -b where trjconv stopped > reading. It seems what ever part of trajectory I choose it ends always at > 1019 frames. Also error (Library file residuetypes.dat not found in) does > not seems to be correct as if it would have been the case then I should not > have got any frame read. > > Thanks for any help > JIom > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] NVE Energy drop in Mixed Precision 4.6.7
Sure, there's drift. But is it significant? What is its value in units of k_B T / dof / ns? How much will such drift affect the quality of your observables? Is that more significant than your other approximations (force field parameterization targets not matching your observables, no polarization, incomplete sampling, lack of replicates)? Is fixing it worth the hit of more than a factor of two in number of samples? It's relatively easy to feel good about solving the one problem that you can solve. But only solve it if it's the one that matters ;-) Mark On Mon, Oct 6, 2014 at 9:03 PM, Johnny Lu wrote: > here is the energy from nve1.edr > http://oi62.tinypic.com/2pqw70l.jpg > > On Mon, Oct 6, 2014 at 3:01 PM, Johnny Lu wrote: > > > Hi. > > > > The system has 9000 water and a ~160 aa amino acid and uses > amber99SB-ildn. > > > > After extensive NPT (300ns, 2ns ts), and then NVT equilibrium (300 ns, > 2ns > > ts), the NVE simulation still has energy drop, despite of the very small > > time step. > > > > Is double precision gromacs the only solution? > > > > The mdp file is: > > > > title = NVT equilibration > > ; Run parameters > > integrator = md; leap-frog integrator > > nsteps = 2950 ; 1 ns > > dt = 0.0002; 0.5 fs > > > > ;NVE > > ;nstcomm = 500 ; remove center of mass motion to reduce energy > and > > temp. drift. > > shake-tol = 0.001 ; shake tolerance. > > verlet-buffer-drift = -1 > > > > > > - Output control > > ;nstxout = 20 ; save coordinates every 1.0 ps > > ;nstvout = 4 ; save velocities every 1.0 ps > > ;nstfout= 20 > > nstenergy = 20 ; save energies every 1.0 ps > > > > nstlog = 1000 ; update log file every 0.2 ps > > ; Bond parameters > > continuation= yes ; Restarting after NVT > > constraint_algorithm = lincs; holonomic constraints > > constraints = all-bonds ; all bonds (even heavy atom-H bonds) > > constrained > > lincs_iter = 4 ; accuracy of LINCS > > lincs_order = 4 ; also related to accuracy > > ; Neighborsearching > > ns_type = grid ; search neighboring grid cells > > nstlist = 40; 10 fs > > rlist = 1.3 ; short-range neighborlist cutoff (in nm) > > rcoulomb= 1.0 ; short-range electrostatic cutoff (in > nm) > > rvdw= 1.0 ; short-range van der Waals cutoff (in > nm) > > ; Electrostatics > > coulombtype = PME ; Particle Mesh Ewald for long-range > > electrostatics > > pme_order = 6 ; cubic interpolation > > fourierspacing = 0.1 ; grid spacing for FFT > > > > ; Temperature coupling is off > > tcoupl = no; modified Berendsen thermostat > > ; Pressure coupling is off > > pcoupl = no > > > > refcoord_scaling = com > > ; Periodic boundary conditions > > pbc = xyz ; 3-D PBC > > ; Dispersion correction > > DispCorr= EnerPres ; account for cut-off vdW scheme > > ; Velocity generation > > gen_vel = no; Velocity generation is off > > cutoff-scheme = Verlet > > > > Thank you in advance. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Gromacs Version 5.0.2 - Bug #1603
On Wed, Oct 8, 2014 at 4:29 PM, Siva Dasetty wrote: > Dear All, > > I am using gpu enabled gromacs version 5.0.2 and I am checking if my > simulation is still affected by bug #1603 > http://redmine.gromacs.org/issues/1603. > > Below is the PP-PME load balancing part of my log file > > PP/PME load balancing changed the cut-off and PME settings: >particle-particlePME > rcoulomb rlistgrid spacing 1/beta >initial 1.000 nm 1.092 nm 108 108 120 0.119 nm 0.320 nm >final1.482 nm 1.574 nm 72 72 80 0.178 nm 0.475 nm > cost-ratio 3.00 0.30 > (note that these numbers concern only part of the total PP and PME load) > > The release notes says, > > If, for your simulation, the final rcoulomb value (1.368 here) is different > from the initial one (1.000 here), then so was the LJ cutoff for > short-ranged interactions, and the model physics was not what you asked > for. > > Does that mean the initial and final values are supposed to be the same? > No. The point of the tuning is to change the rcoulomb value to maximize performance while maintaining the quality of the electrostatic approximation you chose in the .mdp file. If you were using one of the affected versions (5.0 or 5.0.1), then the normal-but-not-guaranteed change of rcoulomb led to an inappropriate change of rvdw, which is why it is a relevant diagnostic for whether an actual simulation from the versions with wrong code was affected in practice. But the normal change of rcoulomb neither confirms nor denies that the bug is fixed in 5.0.2. You could observe that the NPT density in 5.0.2 agrees with a CPU-only (or 4.6.x GPU) calculation, for example. Mark -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Gromacs Version 5.0.2 - Bug #1603
On Wed, Oct 8, 2014 at 8:24 PM, Siva Dasetty wrote: > Thank You Mark for the reply. > > Now that clears my confusion about the values in the PP-PME load part of > the log file. However, I am still a little bit confused about how to > distinguish between a normal-but-not-guranteed change and the normal > change, They're the same thing. It is normal that rcoulomb changes as a result of tuning. But it is not guaranteed to be changed - depends on your simulation setup, CPU, network, phase of the moon... > though I understood that for a normal change we can compare the > densities obtained from GPU runs and the CPU only runs to verify the > results. > > Also, I have a general question about using vdwtype as PME. > > Is it advisable to use vdwtype as PME when I am using GPU runs? > That's two questions in one. LJ-PME with the Verlet scheme runs on GPUs. Whether your simulation should use LJ-PME depends on whether you judge that the effects of inaccurate treatment of long-range inhomogeneity would be noticeable in your system. You should check out the papers cited in the GROMACS manual (and one more is submitted). I personally think the decision is a no-brainer for a membrane+protein system, for example. But for calculating the free-energy of solvation of methanol in water... probably immaterial. Mark > Thanks. > > On Wed, Oct 8, 2014 at 12:42 PM, Mark Abraham > wrote: > > > On Wed, Oct 8, 2014 at 4:29 PM, Siva Dasetty > > wrote: > > > > > Dear All, > > > > > > I am using gpu enabled gromacs version 5.0.2 and I am checking if my > > > simulation is still affected by bug #1603 > > > http://redmine.gromacs.org/issues/1603. > > > > > > Below is the PP-PME load balancing part of my log file > > > > > > PP/PME load balancing changed the cut-off and PME settings: > > >particle-particlePME > > > rcoulomb rlistgrid spacing 1/beta > > >initial 1.000 nm 1.092 nm 108 108 120 0.119 nm 0.320 nm > > >final1.482 nm 1.574 nm 72 72 80 0.178 nm 0.475 nm > > > cost-ratio 3.00 0.30 > > > (note that these numbers concern only part of the total PP and PME > load) > > > > > > The release notes says, > > > > > > If, for your simulation, the final rcoulomb value (1.368 here) is > > different > > > from the initial one (1.000 here), then so was the LJ cutoff for > > > short-ranged interactions, and the model physics was not what you asked > > > for. > > > > > > Does that mean the initial and final values are supposed to be the > same? > > > > > > > No. The point of the tuning is to change the rcoulomb value to maximize > > performance while maintaining the quality of the electrostatic > > approximation you chose in the .mdp file. If you were using one of the > > affected versions (5.0 or 5.0.1), then the normal-but-not-guaranteed > change > > of rcoulomb led to an inappropriate change of rvdw, which is why it is a > > relevant diagnostic for whether an actual simulation from the versions > with > > wrong code was affected in practice. > > > > But the normal change of rcoulomb neither confirms nor denies that the > bug > > is fixed in 5.0.2. You could observe that the NPT density in 5.0.2 agrees > > with a CPU-only (or 4.6.x GPU) calculation, for example. > > > > Mark > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > > > > -- > Siva > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Changing constraints algorithm.
You should start by following all the advice here http://www.gromacs.org/Documentation/Terminology/Blowing_Up Mark On Wed, Oct 8, 2014 at 9:50 PM, Dawid das wrote: > Well, what happens in my system is that water molecule which is actually > near the edge of > solvation box cannot bo settled after ca. 50 ns of simulation. Obviously I > use periodic > boundary conditions. Could you give me any tip about what is wrong if I > provide you > with files you need? If so, what files would you need? > > Best wishes, > Dawid Grabarek > > PS I read samowhere, that it may be due to fact that this water molecule is > hit > by something and this water did not expect it. But I tried to use brutal > force approach > and to restart the calculations couple of times but each time I run into > the same error, > although for different molecule. > > 2014-10-08 13:33 GMT+02:00 Justin Lemkul : > > > > > > > On 10/8/14 7:24 AM, Dawid das wrote: > > > >> Dear gromacs experts, > >> > >> Is it allowed to change constraints algorithm (e.g. from LINCS to SHAKE) > >> during > >> MD simulation? Let's say that simulation crashes because LINCS > constraints > >> are > >> not satisfied. Can I go from LINCS to shake in the middle of simulation > >> and > >> restart calculations from the previous point? > >> > >> > > If LINCS is failing, it's not because you need a different constraint > > algorithm; it's because something physically unrealistic is happening, > and > > the constraints are the first thing to fail. LINCS is more robust than > > SHAKE, so if you're trying to circumvent this problem by moving to SHAKE, > > I'd say it's likely futile. > > > > -Justin > > > > -- > > == > > > > Justin A. Lemkul, Ph.D. > > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > > > Department of Pharmaceutical Sciences > > School of Pharmacy > > Health Sciences Facility II, Room 601 > > University of Maryland, Baltimore > > 20 Penn St. > > Baltimore, MD 21201 > > > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > > http://mackerell.umaryland.edu/~jalemkul > > > > == > > -- > > Gromacs Users mailing list > > > > * Please search the archive at http://www.gromacs.org/ > > Support/Mailing_Lists/GMX-Users_List before posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] v-rescale fatal error
Hi, That results from a recent bug fix. What is in your temperature coupling group? Mark On Oct 10, 2014 6:33 AM, "Kester Wong" wrote: > Dear all, > > > I wanted to use v-rescale thermostat for a NVT run, however, I have been > getting error as such: > > The v-rescale thermostat was called with a group with #DOF=2.999250, but > for #DOF<3 only integer #DOF are supported > > > Has anyone experienced similar issue before? I could not find much > information about it online. > > > > Regards, > > Kester > > > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] v-rescale fatal error
Hi Kester, Glad it's resolved. I am curious what (H3O+?) molecule definition led to that computation of the DOF? That code is not tested at all... Mark On Fri, Oct 10, 2014 at 2:03 PM, Kester Wong wrote: > Hi Justin and all, > > > The same mistake will not be repeated. > > The ions are now defined in the residuetypes.dat file and should be > grouped together. > > > > -From lessons learned, comes better performance. > > Thank you all. > > Kester > - 원본 메일 - > > *보낸사람* : Justin Lemkul > *받는사람* : > *받은날짜* : 2014년 10월 10일(금) 20:38:56 > *제목* : Re: [gmx-users] v-rescale fatal error > > On 10/10/14 7:36 AM, Kester Wong wrote: > > Hi Mark, > > > > > > I think it was due to the charged groups in my temp. coupling setting; I > > had > > the H3O cation(s) and Cl anion(s) grouped separately: > > > > tc-grps = GRA SOL H3O Cl- > > > > ; Time constant (ps) and reference temperature (K) > > > > tau-t= 0.5 0.5 0.5 0.5 > > > > ref-t= 300 300 300 300 > > > > > > Calculations run fine once I grouped the ions together, or water+ions. > > > > You shouldn't couple ions separately from the solvent; that's just not stable. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) > 706-7441http://mackerell.umaryland.edu/~jalemkul > > == > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests > visithttps://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] NVE Energy drop in Mixed Precision 4.6.7
Hi, For what absolute value of energy was the force field parameterized? Mark On Fri, Oct 10, 2014 at 7:38 PM, Johnny Lu wrote: > Well... at that rate, after I run 100 ns, the energy will decrease by 100%. > > On Tue, Oct 7, 2014 at 8:27 AM, Mark Abraham > wrote: > > > Sure, there's drift. But is it significant? What is its value in units of > > k_B T / dof / ns? How much will such drift affect the quality of your > > observables? Is that more significant than your other approximations > (force > > field parameterization targets not matching your observables, no > > polarization, incomplete sampling, lack of replicates)? Is fixing it > worth > > the hit of more than a factor of two in number of samples? > > > > It's relatively easy to feel good about solving the one problem that you > > can solve. But only solve it if it's the one that matters ;-) > > > > Mark > > > > On Mon, Oct 6, 2014 at 9:03 PM, Johnny Lu > wrote: > > > > > here is the energy from nve1.edr > > > http://oi62.tinypic.com/2pqw70l.jpg > > > > > > On Mon, Oct 6, 2014 at 3:01 PM, Johnny Lu > > wrote: > > > > > > > Hi. > > > > > > > > The system has 9000 water and a ~160 aa amino acid and uses > > > amber99SB-ildn. > > > > > > > > After extensive NPT (300ns, 2ns ts), and then NVT equilibrium (300 > ns, > > > 2ns > > > > ts), the NVE simulation still has energy drop, despite of the very > > small > > > > time step. > > > > > > > > Is double precision gromacs the only solution? > > > > > > > > The mdp file is: > > > > > > > > title = NVT equilibration > > > > ; Run parameters > > > > integrator = md; leap-frog integrator > > > > nsteps = 2950 ; 1 ns > > > > dt = 0.0002; 0.5 fs > > > > > > > > ;NVE > > > > ;nstcomm = 500 ; remove center of mass motion to reduce > energy > > > and > > > > temp. drift. > > > > shake-tol = 0.001 ; shake tolerance. > > > > verlet-buffer-drift = -1 > > > > > > > > > > > > - Output control > > > > ;nstxout = 20 ; save coordinates every 1.0 ps > > > > ;nstvout = 4 ; save velocities every 1.0 ps > > > > ;nstfout= 20 > > > > nstenergy = 20 ; save energies every 1.0 ps > > > > > > > > nstlog = 1000 ; update log file every 0.2 ps > > > > ; Bond parameters > > > > continuation= yes ; Restarting after NVT > > > > constraint_algorithm = lincs; holonomic constraints > > > > constraints = all-bonds ; all bonds (even heavy atom-H bonds) > > > > constrained > > > > lincs_iter = 4 ; accuracy of LINCS > > > > lincs_order = 4 ; also related to accuracy > > > > ; Neighborsearching > > > > ns_type = grid ; search neighboring grid cells > > > > nstlist = 40; 10 fs > > > > rlist = 1.3 ; short-range neighborlist cutoff (in > > nm) > > > > rcoulomb= 1.0 ; short-range electrostatic cutoff > (in > > > nm) > > > > rvdw= 1.0 ; short-range van der Waals cutoff > (in > > > nm) > > > > ; Electrostatics > > > > coulombtype = PME ; Particle Mesh Ewald for long-range > > > > electrostatics > > > > pme_order = 6 ; cubic interpolation > > > > fourierspacing = 0.1 ; grid spacing for FFT > > > > > > > > ; Temperature coupling is off > > > > tcoupl = no; modified Berendsen thermostat > > > > ; Pressure coupling is off > > > > pcoupl = no > > > > > > > > refcoord_scaling = com > > > > ; Periodic boundary conditions > > > > pbc = xyz ; 3-D PBC > > > > ; Dispersion correction > > > > DispCorr= EnerPres ; account for cut-off vdW scheme > > > > ; Velocity generation > > > > gen_vel = no; Velocity generation is off > > > > cutoff-scheme = Verlet > > > > > > > > Thank you in advance. > >
Re: [gmx-users] Performance degradation for Verlet cutoff-scheme compared to group
On Fri, Oct 10, 2014 at 8:16 PM, Олег Титов wrote: > Good day. > > I've got sigmificant performance degradation when trying to use Verlet > cutoff-scheme for free energy calculation. My system contains 1 > bromobenzene molecule and 543 TIP3P waters. 16 hours of calculation on > 8-core CPU resulted in 2.5 ns trajectory. With group scheme i've got 6.5 ns > trajectory in 7h 40 min. > > Interesting that with group scheme gromacs tells me that it was using 8 MPI > threads while with Verlet - 1 MPI and with 8 OpenMP threads. Both times > I've launched the calculation with "mdrun -deffnm test". > One scheme supports OpenMP, one doesn't... > I believe that this is caused by "plain C kernels" as GROMACS warns me. Is > there any possibility to overcome this issue? > Yes... > I have access only to old gcc 4.1.2 (without SSE4.1) and buggy icc 11.1 on > this machine. > Gromacs requires a real compiler to get performance, like the install guide says. You need to get one. Mark > Thanks for your help. > > Oleg Titov > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Use NVT to mimic NVE
On Fri, Oct 10, 2014 at 7:41 PM, Johnny Lu wrote: > Hi. > > Is it a good idea to mimic NVE by a NVT simulation with a large temperature > coupling time constant, to reduce the effect of the thermostat ? > Not if your observable is the total energy. But for most interesting observables, this is more than fine. > If I use V-rescale thermostat, what artifacts will the simulation get if I > use a large coupling time (say, 500 ps) and single precision gromacs ? > Probably nobody knows :-) Thermodynamic ensemble differences disappear as the system becomes large. But quantifying that from converged ensembles for a given observable is work. Mark > Thank you. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Performance degradation for Verlet cutoff-scheme compared to group
Hi, Very likely that simulation is too small to make good use of that many cores (though if there's hyper-threading going on, then there may only be 8 real cores, and you may do better with hyper-threading off...). Gromacs use of OpenMP does not do very well with lots of threads and few atoms. If you share a link to a log file on a file-sharing service, there might be relevant observations people could make. If running multiple replicates of your simulation is a sensible thing to do, you will likely get much better value from your hardware by running several such simulations per node (e.g. with mdrun_mpi -multi) Mark On Mon, Oct 13, 2014 at 10:55 AM, Олег Титов wrote: > Thanks for you reply. > > On a different machine I've recompiled GROMACS with icc version 13.1.0 (gcc > version 4.4.6 compatibility). > cmake command: > I_MPI_CC=nvcc CC=icc CXX=icpc cmake ../gromacs-src > -DCMAKE_INSTALL_PREFIX=~/gromacs-5.0.2/ -DGMX_FFT_LIBRARY=MKL -DGMX_MPI=OFF > -DGMX_GPU=OFF -DGMX_BUILD_MDRUN_ONLY=ON -DGMX_DEFAULT_SUFFIX=OFF > -DGMX_BINARY_SUFFIX=_intel -DGMX_LIBS_SUFFIX=_intel > > This simulation took 10 hours on 16 CPU cores (15.5 ns/day). Is this normal > performance for a system with 1641 atoms? > > 2014-10-11 1:21 GMT+04:00 Mark Abraham : > > > On Fri, Oct 10, 2014 at 8:16 PM, Олег Титов > > wrote: > > > > > Good day. > > > > > > I've got sigmificant performance degradation when trying to use Verlet > > > cutoff-scheme for free energy calculation. My system contains 1 > > > bromobenzene molecule and 543 TIP3P waters. 16 hours of calculation on > > > 8-core CPU resulted in 2.5 ns trajectory. With group scheme i've got > 6.5 > > ns > > > trajectory in 7h 40 min. > > > > > > Interesting that with group scheme gromacs tells me that it was using 8 > > MPI > > > threads while with Verlet - 1 MPI and with 8 OpenMP threads. Both times > > > I've launched the calculation with "mdrun -deffnm test". > > > > > > > One scheme supports OpenMP, one doesn't... > > > > > > > I believe that this is caused by "plain C kernels" as GROMACS warns me. > > Is > > > there any possibility to overcome this issue? > > > > > > > Yes... > > > > > > > I have access only to old gcc 4.1.2 (without SSE4.1) and buggy icc 11.1 > > on > > > this machine. > > > > > > > Gromacs requires a real compiler to get performance, like the install > guide > > says. You need to get one. > > > > Mark > > > > > > > Thanks for your help. > > > > > > Oleg Titov > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > posting! > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > * For (un)subscribe requests visit > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > > send a mail to gmx-users-requ...@gromacs.org. > > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] same input tpr same results?
No. http://www.gromacs.org/Documentation/Terminology/Reproducibility Mark On Mon, Oct 13, 2014 at 8:32 AM, Albert wrote: > Hello: > > I've generate a .tpr file in my local machine and I am going to submit it > to different cluster. I am just wondering, will the trajectory exactly the > same? > > thank you very much > > albert > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Redirecting trajectories from one gmx module to another
Hi, Unfortunately, Gromacs file handling wasn't designed with pipes in mind. In particular, we often open a file, read its header to get some information, and then go back and read the file again, which doesn't work well with using pipes (see http://redmine.gromacs.org/issues/1489 for details). Relaxing that would be very useful, but there's nobody currently working on it. Work-arounds might include memory-mapping the temporary file, or doing the analysis on pieces and combining the analysis results, but there's no magic bullet. Mark On Mon, Oct 13, 2014 at 10:32 AM, Machtens, Jan-Philipp < j.macht...@fz-juelich.de> wrote: > Hi, > I would like to redirect gromacs trajectories from one gmx module to > another, e.g. using a shell pipe... > For example, analyzing a trajectory which is split into two files could be > done > using > gmx trjcat -f traj.part1.xtc traj.part2.xtc -o traj.cat.xtc && gmx > whatever -f traj.cat.xtc -o result > I would like to save the time needed by the trjcat run and the additional > disk space for the concatenated trajectory by using something like > gmx trjcat -f traj.part1.xtc traj.part2.xtc | gmx whatever -f - -o result > > This doesn't work that easy. Does anyone know an existing solution ? > Thanks! > Jan-Philipp > > > > > > > Forschungszentrum Juelich GmbH > 52425 Juelich > Sitz der Gesellschaft: Juelich > Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 > Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher > Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), > Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, > Prof. Dr. Sebastian M. Schmidt > > > > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Use NVT to mimic NVE
Hi, What is your target observable? What "got worse?" Mark On Mon, Oct 13, 2014 at 11:17 PM, Johnny Lu wrote: > The simulation get worse in a new way. > > I see that thermostat scales velocity and may not fix numerical error in > potential energy. > > On Mon, Oct 13, 2014 at 2:07 PM, Johnny Lu wrote: > > > I just want something that will patch up the energy lost due to numerical > > error of NVE simulation of the system ran by mixed precision gromacs, > > instead of a thermostat. > > > > I hope the velocity rescaling is sufficiently uncorrelated with the > motion > > of the protein. > > > > So far, the simulations ran 2.5 ns, and the fluctuation of total energy > > seems to be within 1% of total energy, with a 100ps or 1ns coupling > > constant. > > > > May be I should try a 10 ns coupling constant, just to see if the > > simulation would go belly up. > > > > On Mon, Oct 13, 2014 at 11:02 AM, Michael Shirts > > wrote: > > > >> > I guess, if I pick a coupling constant that is just small enough to > >> keep the > >> energy conserved, I would get a NVT simulation that is as close as a NVE > >> simulation as possible. > >> > >> > Is this correct? > >> > >> Yes, but then at that point the thermostat isn't actually > thermostatting. > >> The Bussi comment is merely to show that his thermostat correctly > reduces > >> to Newton's law in the limit, not that it would be useful to run it in > >> that > >> limit. > >> > >> On Mon, Oct 13, 2014 at 10:28 AM, Johnny Lu > >> wrote: > >> > >> > On page 014101-3, the Bussi paper ( > http://dx.doi.org/10.1063/1.2408420) > >> > mentioned: "On the other hand, for coupling constant approaching > >> > infinity,the Hamiltonian dynamics is recovered." > >> > Does that means that for a large enough coupling constant, the > >> velocities > >> > are nearly not rescaled, and the dynamics (like rate of motion) would > be > >> > same as that of NVE? > >> > > >> > A larger coupling constant, means a smaller diffusion coefficient in > the > >> > axillary dynamics by equation 6. > >> > > >> > While the effects of the velocity rescaling at each step will > >> accumulate, a > >> > larger coupling constant means the thermostat perturb less of the > >> dynamics, > >> > and the resulting dynamics is closer to a NVE simulation. > >> > There is no worry that the thermostat would suddenly rescale the > >> dynamics > >> > every x step, because in the procedure of the thermostat, the > velocities > >> > are rescaled every step, regardless of the coupling constant. > >> > > >> > I guess, if I pick a coupling constant that is just small enough to > keep > >> > the energy conserved, I would get a NVT simulation that is as close > as a > >> > NVE simulation as possible. > >> > > >> > Is this correct? > >> > -- > >> > Gromacs Users mailing list > >> > > >> > * Please search the archive at > >> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >> > posting! > >> > > >> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > > >> > * For (un)subscribe requests visit > >> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >> > send a mail to gmx-users-requ...@gromacs.org. > >> > > >> -- > >> Gromacs Users mailing list > >> > >> * Please search the archive at > >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >> posting! > >> > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > >> * For (un)subscribe requests visit > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >> send a mail to gmx-users-requ...@gromacs.org. > >> > > > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Using Gpus on multiple nodes. (Feature #1591)
On Tue, Oct 14, 2014 at 10:51 PM, Siva Dasetty wrote: > Dear All, > > I am currently able to run simulation on a single node containing 2 gpus, > but I get the following fatal error when I try to run the simulation using > multiple gpus (2 on each node) on multiple nodes (2 for example) using OPEN > MPI. > Here you say you want 2 ranks on each of two nodes... > Fatal error: > > Incorrect launch configuration: mismatching number of PP MPI processes and > GPUs > > per node. > > mdrun was started with 4 PP MPI processes per node, ... but here mdrun means what it says... > but you provided only 2 > GPUs. > > The command I used to run the simulation is > > mpirun -np 4 mdrun -s -deffnm <...> -gpu_id 01 > ... which means your MPI environment (hostfile, job script settings, whatever) doesn't have the settings you think it does, since it's putting all 4 ranks on one node. Mark > > > However It at least runs if I use the following command, > > > mpirun -np 4 mdrun -s -deffnm <...> -gpu_id 0011 > > > But after referring to the following thread, I highly doubt if I am using > all the 4 gpus available in the 2 nodes combined. > > > > https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-developers/2014-May/007682.html > > > > Thank you for your help in advance, > > -- > Siva > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Problem implementing REST
Hi, What GROMACS version is this? What bits of your topology are being complained about? Mark On Thu, Oct 16, 2014 at 11:12 AM, carlo martinotti < specialken...@hotmail.com> wrote: > I'm currently trying to implement Replica Exchange with Solute Tempering > in gromacs, as previously done by terakawa et al (On easy implementation of > a variant of the replica exchange with solute tempering in GROMACS, J > Comput Chem. 2011 May;32(7):1228-34. doi: 10.1002/jcc.21703. Epub 2010 Nov > 29.) > From what i understood you have to change ffnonbonded.itp adding new > atomtypes with perturbed LJ parameters, then change ffbonded.itp adding new > bond/angles and dihedral types between this perturbed atoms with modifed > harmonic constant, and that's it for the forcefield. > Then you have to prepare a topology with state A and state B with state B > having perturbed charges and the atom types corresponding to the perturbed > version of the state A atoms. > Now, i have some problems. I'm trying to modify amber03 forcefield, but > when i try to run grompp it gives me this errors: > > ERROR 1 [file topol.top, line 199]: Cannot automatically perturb a > torsion with multiple terms to different form. Please specify perturbed > parameters manually for this torsion in your topology! > ERROR 2 [file topol.top, line 202]: Cannot automatically perturb a > torsion with multiple terms to different form. Please specify perturbed > parameters manually for this torsion in your topology! > > ERROR 3 [file topol.top, line 205]: Cannot automatically perturb a > torsion with multiple terms to different form. Please specify perturbed > parameters manually for this torsion in your topology! > > ERROR 4 [file topol.top, line 206]: Cannot automatically perturb a > torsion with multiple terms to different form. Please specify perturbed > parameters manually for this torsion in your topology! > Now, it seems that gromacs can't do this operation with amber, but in the > article that i read they actually used amber03, so what should i do? This > are my files mdp top ffbonded ffnonbonded > Can somebody explain me where is the problem? > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Problem implementing REST
Hi, Thanks for the links. Offhand, I don't know the answers to your questions and don't have time to look into it now. You should certainly ask them how they did it. One work-around might be to do the necessary trig to convert sums-of-Fourier dihedrals to a Ryckaert-Bellemans dihedral, and the issue of type 9 and lambda interpolation goes away. Mark On Thu, Oct 16, 2014 at 3:03 PM, carlo martinotti wrote: > I'm running GROMACS version 4.6.3, it seems that the hyperlinks doesn't > work in the mailing list, so i'll post the links to my files (perturbed > atoms are indicated by the "&"): > mdp > http://textuploader.com/oj7qtop > > http://textuploader.com/oj7cffbonded > > http://textuploader.com/oj7mffnonbonded > http://textuploader.com/oj7h > The issue seems to be regargind lines in topology which correspond to > proper dihedrals (function 9). Actually i've gone in the ffbonded file and > i tried to delete the perturbed proper dihedrals, but then again it would > give one error and one warning for each of the dihedrals as this one : > > ERROR 48 [file topol2.top, line 222]: Cannot automatically perturb a > torsion with multiple terms to different form. Please specify perturbed > parameters manually for this torsion in your topology! > > WARNING 48 [file topol2.top, line 222]: No default Proper Dih. types for > perturbed atoms, using normal values > > The problem seems to be as it follows: > The author in the article claims to have made everything with the lambda > system , but lambda system seems not able to perturb dihedrals with > multiple terms, nor to use the same terms in state A and B. So, can i solve > the problem and still use lambda system to interpolate betwen the 2 > hamiltonians? > In case i can't, can i build one complete topology file for each replica > that i want to simulate, perturb the topology modifying the hamiltonian > consequently and then run a replica exchange with the REMD routine? > Wouldn't it be the same thing as using the lambda system, except it would > be better because you can use verlet cutoff scheme, and so, also, GPUs? > > > > Date: Thu, 16 Oct 2014 12:04:38 +0200 > > From: mark.j.abra...@gmail.com > > To: gmx-us...@gromacs.org > > Subject: Re: [gmx-users] Problem implementing REST > > > > Hi, > > > > What GROMACS version is this? What bits of your topology are being > > complained about? > > > > Mark > > > > On Thu, Oct 16, 2014 at 11:12 AM, carlo martinotti < > > specialken...@hotmail.com> wrote: > > > > > I'm currently trying to implement Replica Exchange with Solute > Tempering > > > in gromacs, as previously done by terakawa et al (On easy > implementation of > > > a variant of the replica exchange with solute tempering in GROMACS, J > > > Comput Chem. 2011 May;32(7):1228-34. doi: 10.1002/jcc.21703. Epub 2010 > Nov > > > 29.) > > > From what i understood you have to change ffnonbonded.itp adding new > > > atomtypes with perturbed LJ parameters, then change ffbonded.itp > adding new > > > bond/angles and dihedral types between this perturbed atoms with > modifed > > > harmonic constant, and that's it for the forcefield. > > > Then you have to prepare a topology with state A and state B with > state B > > > having perturbed charges and the atom types corresponding to the > perturbed > > > version of the state A atoms. > > > Now, i have some problems. I'm trying to modify amber03 forcefield, but > > > when i try to run grompp it gives me this errors: > > > > > > ERROR 1 [file topol.top, line 199]: Cannot automatically perturb a > > > torsion with multiple terms to different form. Please specify > perturbed > > > parameters manually for this torsion in your topology! > > > ERROR 2 [file topol.top, line 202]: Cannot automatically perturb a > > > torsion with multiple terms to different form. Please specify > perturbed > > > parameters manually for this torsion in your topology! > > > > > > ERROR 3 [file topol.top, line 205]: Cannot automatically perturb a > > > torsion with multiple terms to different form. Please specify > perturbed > > > parameters manually for this torsion in your topology! > > > > > > ERROR 4 [file topol.top, line 206]: Cannot automatically perturb a > > > torsion with multiple terms to different form. Please specify > perturbed > > > parameters manually for this torsion in your topology! > > > Now, it seems that gromacs can't do this operation with amber, but in > the > > > article that i read they actually used amber03, so what should i do? > This > > > are my files mdp top ffbonded ffnonbonded > > > Can somebody explain me where is the problem? > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > posting! > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > * For (un)subscribe requests visit > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > > send a m
Re: [gmx-users] Conserved energy ("Conserved En.") in NVT simulation
On Tue, Oct 14, 2014 at 4:32 PM, Wade wrote: > Dear Mark and ALL, >I am trying to calculate the conserved energy (H-tilde) in Bussi's > stochastic velocity rescale algorithm (jcp,2007). > In previous maillist, Mark had mentioned that the conserved En. in ener > file is the H in bussi's paper ( > http://permalink.gmane.org/gmane.science.biology.gromacs.user/63005). > According to the eq. 15 in Bussi's paper, we just need to get the time > integration of dK if we have had the H. > I carefully checked the coupling.c file, and noticed a variable - > therm_integral[i] in the fucntion vrescale_tcoupl(). > The therm_integral[i]-= Ek_new - Ek. It seems like an accumulation of the > -dK. > If it realy is the sum of -dK, the problem could become simple. > That could well be true. I did look carefully at the code earlier this year, and decided it was correct and wrote output of sensible things. However I don't remember whether the conserved quantity reported is H or H-tilde, and don't have time now to go back. But IIRC because one of them has a time dependence, you can run double-precision GROMACS in a conservative NVE setup and observe no drift, then add this thermostat, and from that run you will know which of H and H-tilde is reported as the conserved quantity. Mark What we need to do is just like this: H-tilde=H-Tau-t* therm_integral[i].? > Is that right? I really need your help. > Any suggestion is valuable. > > Wade > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Multiple writing to same trajectory issue
On Thu, Oct 16, 2014 at 5:04 PM, Matthias Ernst < matthias.er...@physik.uni-freiburg.de> wrote: > Dear users, > > I usually resume calculation of a trajectory from a checkpoint file > appending to the old files (which, as I learned, is obviously not a good > idea..). > It's brittle in the case of things going wrong... but if you want full backups, or proper transactional semantics on your files, then you're going to need to participate in the process. Various mdrun command-line options are available to help with this, but we can't have "save every checkpoint" as the default behaviour. Defaulting to mdrun -noappend is not great either ... "concatenate all your files before every analysis," or "provide all files to every analysis tool," are not fun kinds of workflows for users (or implementers). Due to some issue with our queueing system, several jobs that were > marked as depending on each other started at once and all wrote at the > same trajectory file. I noticed this only 10 hours later. > Well, they opened the same file for writing, but what happens in such a case surely depends on the file system implementation. What does Gromacs do if a time frame is written to a trajectory that > already has this time? Is it doubled or discarded? mdrun doesn't even know. It says "write a frame" and if the file system implements "everybody with the file open for writing can write to it in some order," or "only the first opener can write," or "only the last opener can write," or "only a random process can write," or "subsequent openers cann't get a file handle so probably they get an error condition," then the result conforms with whatever the implementation does. All kinds of software share the same limitation, of course. gmx check can perhaps help with the detective work about what did happen and whether stuff is now broken. And the same for the > other files (log/edr...)? > Same, but whether the results on disk are mutually consistent depends on the above... I think using trjconv with -e option just until the timestep of the > multiple writing should recover at least the data gained until then, but > is there a possibility to recover and resume my run at that point? > Only if there is still a matching checkpoint file from that time, which would only be true if the resumed runs didn't proceed very far, or you kept a backup somehow. Mark > > Thanks for your help, > Matthias > > > -- > Progress... http://www.phdcomics.com/comics/archive.php?comicid=1611 > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Not achieving any speedup using Open MPI
Hi, You should only attempt this if the machines running MPI have homogeneous hardware, otherwise the faster ones just wait for the slower ones. So, assuming you have two near-identical machines, you can do a diff of the single-node and dual-node log files and observe what mdrun is probably complaining about in the two cases. Mark On Fri, Oct 17, 2014 at 5:05 PM, Rytis Slatkevičius wrote: > I am not mixing OpenMP with MPI; it runs one process per core and all are > communicating via Open MPI. Mixing these was indeed even slower. > > -- > Pagarbiai / Sincerely > Rytis Slatkevičius > +370 670 7 > > On Fri, Oct 17, 2014 at 5:42 PM, Johnny Lu wrote: > > > i heard that mixing mpi and open mp together is bad idea (run more slow), > > unless the simulation has large number of atoms, and use many cpu. > > > > May be comparing gromacs running on a single computer, with and without > > openmp will show a difference in speed. > > > > On Fri, Oct 17, 2014 at 10:05 AM, Da-Wei Li wrote: > > > > > For a system with only ~20K atoms and you are using normal LAN, I feel > > your > > > result is not unexpected. > > > > > > dawei > > > > > > On Fri, Oct 17, 2014 at 9:20 AM, Rytis Slatkevičius > > > > wrote: > > > > > > > Hello, > > > > > > > > first of all: I am not a scientist, but rather an IT person trying to > > set > > > > up Gromacs for fellow scientists. My goal is to set up Gromacs on > > several > > > > local computers (connected with 1gbps LAN) and achieve some speedup > of > > > our > > > > runs using MPI. > > > > > > > > I have installed Gromacs 5.0.2 from Debian repository (package > > > > gromacs-openmpi). I can run Gromacs over multiple computers, I see > > > > processes being spooled up, so MPI itself is working. However, I am > not > > > > seeing any speedup at all - in fact, I get a significant slowdown. > > > > > > > > When running on a rather old dualcore laptop, I can finish a d.lzm > run > > > from > > > > http://www.gromacs.org/About_Gromacs/Benchmarks within 109s or so. > If > > I > > > > add > > > > a quadcore machine into the mix, I would expect the computation to be > > > much > > > > faster - but instead I finish everything within 139 seconds! The > > quadcore > > > > can finish the job in 45 seconds when running on its own without Open > > > MPI. > > > > > > > > I can't wrap my head around what I am doing wrong. My command line > is: > > > > > > > > mpirun --display-map --hostfile hosts mdrun_mpi -v -deffnm d.lzm -dlb > > yes > > > > > > > > Any help would be appreciated. > > > > > > > > -- > > > > Pagarbiai / Sincerely > > > > Rytis Slatkevičius > > > > +370 670 7 > > > > -- > > > > Gromacs Users mailing list > > > > > > > > * Please search the archive at > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > > posting! > > > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > * For (un)subscribe requests visit > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or > > > > send a mail to gmx-users-requ...@gromacs.org. > > > > > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > posting! > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > * For (un)subscribe requests visit > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > > send a mail to gmx-users-requ...@gromacs.org. > > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Not achieving any speedup using Open MPI
That benchmark is using the group scheme, which started to lose parallel efficiency with Infiniband at around 1000 atoms/core, but YMMV greatly. That number will go up for gigabit ethernet. There's no point sharing the workload if the communication latency becomes comparable with the compute time, of course. Mark On Fri, Oct 17, 2014 at 5:36 PM, Rytis Slatkevičius wrote: > Thanks; what do you think would be a good number of atoms to expect actual > speedup? > > -- > Pagarbiai / Sincerely > Rytis Slatkevičius > +370 670 7 > > On Fri, Oct 17, 2014 at 5:05 PM, Da-Wei Li wrote: > > > For a system with only ~20K atoms and you are using normal LAN, I feel > your > > result is not unexpected. > > > > dawei > > > > On Fri, Oct 17, 2014 at 9:20 AM, Rytis Slatkevičius > > wrote: > > > > > Hello, > > > > > > first of all: I am not a scientist, but rather an IT person trying to > set > > > up Gromacs for fellow scientists. My goal is to set up Gromacs on > several > > > local computers (connected with 1gbps LAN) and achieve some speedup of > > our > > > runs using MPI. > > > > > > I have installed Gromacs 5.0.2 from Debian repository (package > > > gromacs-openmpi). I can run Gromacs over multiple computers, I see > > > processes being spooled up, so MPI itself is working. However, I am not > > > seeing any speedup at all - in fact, I get a significant slowdown. > > > > > > When running on a rather old dualcore laptop, I can finish a d.lzm run > > from > > > http://www.gromacs.org/About_Gromacs/Benchmarks within 109s or so. If > I > > > add > > > a quadcore machine into the mix, I would expect the computation to be > > much > > > faster - but instead I finish everything within 139 seconds! The > quadcore > > > can finish the job in 45 seconds when running on its own without Open > > MPI. > > > > > > I can't wrap my head around what I am doing wrong. My command line is: > > > > > > mpirun --display-map --hostfile hosts mdrun_mpi -v -deffnm d.lzm -dlb > yes > > > > > > Any help would be appreciated. > > > > > > -- > > > Pagarbiai / Sincerely > > > Rytis Slatkevičius > > > +370 670 7 > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > posting! > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > * For (un)subscribe requests visit > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > > send a mail to gmx-users-requ...@gromacs.org. > > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Conserved energy ("Conserved En.") in NVT simulation (Wade)
On Sat, Oct 18, 2014 at 4:32 PM, Wade wrote:
> Dear Mark,
> Thank your very much for your reply. However, I still confused because
> results showed that the conserved En. was time dependent (with small
> fluctuation); but, the total energy in the ener file has small drift with
> high fluctuations.
>
"Both these things vary" doesn't mean anything. Numbers, or it didn't
happen ;-)
> Further, I rechecked the code (gmx-4.5.5) ?in these days, and I noticed a
> part of code might be useful ("enerd->term[F_ECONSERVED] =
> enerd->term[F_ETOT] + compute_conserved_from_auxiliary(ir,state,&MassQ);").
> It will be actived when the leap-frog integrator is employed.
> To assure the the conserved En. is either H or H-tilde, I changed the code
> as this: "enerd->term[F_ECONSERVED] = enerd->term[F_ETOT];". Result shown
> that the "total energy" and "conserved En." are same now in the output of
> ener file?.
>
Great. A = A...
> Dose it means that the conserved En. in ener file is H-tilde?
>
...which doesn't say what B is... The question is whether there's an
intrinsic time dependence on the value returned by
compute_conserved_from_auxiliary. You can only do that by removing the
*other* term.
>
> ?
>
> If yes, why does the conserved En. drifted with a constant rate in a 10 ns
> ?simulation for a pure water box (216 tip4p water)?
>
>
Because it's characteristic of the drift of your setup or of the
implementation of what is reported as the conserved quantity. I suggested a
diagnostic procedure. Did you try it? If not, why not?
Mark
With best wishes,
>
>
> Wade
>
>
> (part of the code please see below, I hope I have got the key point).
> ?
>
> ~
> /* # BEGIN PREPARING EDR OUTPUT ### */
> /* sum up the foreign energy and dhdl terms */
> sum_dhdl(enerd,state->lambda,ir); /* use the directly determined
> last velocity, not actually the averaged half steps */if (bTrotter
> && ir->eI==eiVV) {enerd->term[F_EKIN] = last_ekin;
> }enerd->term[F_ETOT] = enerd->term[F_EPOT] +
> enerd->term[F_EKIN];if (bVV){
> enerd->term[F_ECONSERVED] = enerd->term[F_ETOT] +
> saved_conserved_quantity;}else {
> enerd->term[F_ECONSERVED] = enerd->term[F_ETOT] +
> compute_conserved_from_auxiliary(ir,state,&MassQ);?
>
> ~~
>
>
>
>
>
>
>
>
>
>
> >That could well be true. I did look carefully at the code earlier this
> >year, and decided it was correct and wrote output of sensible things.
> >However I don't remember whether the conserved quantity reported is H or
> >H-tilde, and don't have time now to go back. But IIRC because one of them
> >has a time dependence, you can run double-precision GROMACS in a
> >conservative NVE setup and observe no drift, then add this thermostat, and
> >from that run you will know which of H and H-tilde is reported as the
> >conserved quantity.
>
> >Mark
>
> > Is that right? I really need your help.
> > Any suggestion is valuable.
> >
> > Wade?
> > --
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
--
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Re: [gmx-users] Understanding comments in pdb2gmx output
On Sat, Oct 18, 2014 at 9:59 PM, Agnivo Gosai wrote: > Dear Users > > Thrombin-Aptamer complex : PDB ID 1HAO > > Thanks for the earlier comments. I appreciate the efforts of all users and > developers for taking their time out and helping. > > I checked the pdb file for the "occupancies" not equal to 1.000 and found 9 > atoms having 0.001 ocuupancy. So, I manually changed the values to 1.000. > You should understand and resolve the reason for the warning, not just suppress the symptoms. That means reading the PDB file to find out why the occupancies are not one. I expect you will find that the long bond and these residues are related. Mark As , Mr. Lu and Dr. Lemkul said I checked for multiple conformations in the > protein part but found out that 0.001 occupancy was assigned to 9 atoms in > the 15-mer oligonucleotide (aptamer) part. > The residue names were DT. > > After this , I again passed the curated pdb through pdb2gmx and cam across > the following warning :- > ### > Generating any missing hydrogen atoms and/or adding termini. > Now there are 253 residues with 4078 atoms > Chain time... > Making bonds... > Warning: Long Bond (2429-2431 = 0.805851 nm) > Number of bonds was 4137, now 4136 > # > > Now Dr. Lemkul earlier said that there can be missing atoms or a very bad > geometry. I also thought it could be regarding the earlier warning on > occupancies. However this "long bond" warning is still showing up. Does > anyone have any idea as to how to fix this ? Is it possible to do it > manually ? In the expression 2429 - 2431 = 0.805851 nm are the 1st two nos. > atom nos ?? > Am I facing this issue because I manually deleted one ligand (inhibitor) > bound to the active site of the thrombin protein and also manually removed > all lines containing HOH ( crystallized water ) ? > > I checked the GROMACS online help and it talks about missing atoms , there > is no missing atom warning in pdb2gmx output !! > < > I am copy pasting two other blocks , as I am unable to understand their > meaning :- > > > # > WARNING: all CONECT records are ignored > Read 'DNA 5'-D(*GP*GP*TP*TP*GP*GP*TP*GP*TP*GP*GP*TP*TP*GP*G)-3'; ; > ALPHA-THROMBIN LIGHT CHAIN; ALPHA-THROMBIN HEAVY CHAIN', 2590 atoms > Analyzing pdb file > Splitting chemical chains based on TER records or chain id changing. > There are 3 chains and 0 blocks of water and 247 residues with 2590 atoms > > chain #res #atoms > 1 'D'15315 > 2 'L'27222 > 3 'H' 253 2053 > All occupancies are one > > *What is the meaning of this warning ???* In the web , I found a post > saying for proteins it is ok , but I also have DNA in my system. Any > suggestions ? > > # > Writing topology > Including chain 1 in system: 488 atoms 15 residues > Including chain 2 in system: 449 atoms 27 residues > Including chain 3 in system: 4078 atoms 253 residues > Now there are 5015 atoms and 295 residues > Total mass in system 37060.423 a.m.u. > Total charge in system -11.000 e > > *Now , the number of residues have increased and the total no. of atoms > have also increased.* *I have also observed the same thing while completing > Dr. Lemkul's tutorials. Why does this happen ? I have searched the web but > could not find any satisfactory answer.* > > Thanks & Reagrds > Agnivo Gosai > Graduate Student > Iowa State University > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] pressure dependence on volume.
On Sun, Oct 19, 2014 at 4:18 PM, Johnny Lu wrote: > The averaged volume of the 1bar pressure NPT simulation over 150ns was very > clearly 298.5 nm^3. > But now, when I set the volume of the NVT simulation to 298.7 nm^3 by > starting from a NPT frame that has the volume, the average was 1.2 bar with > error estimate 0.53, over 52 ns. > ... so, indistiguishable from a wide range true values near 1 bar. No big surprise there. http://www.gromacs.org/Documentation/Terminology/Pressure The same tactic also didn't work for a 300 ns NPT simulation and > subsequently 300 ns NVT simulation. This NVT simulation pressure was > averaged to be around 4 bar. > > Why starting a NVT simulation from a NPT frame with the averaged NPT volume > didn't give the target pressure of 1 bar? Because that expectation is unreasonable for this system size over this time scale :-) Mark > On Sun, Oct 19, 2014 at 2:20 AM, Tsjerk Wassenaar > wrote: > > > Hi Johnny, > > > > The density is M/V. The only parameter changing with pressure coupling is > > V, so the density and volume are fully correlated. No surprise there. > > > > Cheers, > > > > Tsjerk > > On Oct 19, 2014 2:27 AM, "Johnny Lu" wrote: > > > > > The frames with density closest to the average density also have > volumes > > > closest to the averaged volume. > > > > > > On Sat, Oct 18, 2014 at 8:18 PM, Johnny Lu > > wrote: > > > > > > > I searched the energy file made by g_energy, and found that NPT > frames > > > > with very similar densities have very similar volume. > > > > > > > > So, I guess using density is same as using volume in this case. > > > > > > > > On Sat, Oct 18, 2014 at 9:09 AM, Johnny Lu > > > wrote: > > > > > > > >> Would manually setting the box size make vacuum bubbles? > > > >> > > > >> On Sat, Oct 18, 2014 at 9:08 AM, Johnny Lu > > > >> wrote: > > > >> > > > >>> my bad. that formula for density is wrong. But I till don't see why > > > >>> using the same averaged density (instead of volume) for the NVT and > > NPT > > > >>> simulations would give a different result. > > > >>> > > > >>> On Sat, Oct 18, 2014 at 8:52 AM, Johnny Lu > > > > >>> wrote: > > > >>> > > > Was the density calculated by # particles / volume ? > > > > > > If so, using volume (as I did), and using density would give the > > same > > > wrong pressure, upon transitioning from NPT to NVT. > > > > > > >>> > > > >>> > > > >> > > > > > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > posting! > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > * For (un)subscribe requests visit > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > > send a mail to gmx-users-requ...@gromacs.org. > > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] charge group moved too far between two domain decomposition steps?
Hi, You should start by using a time step more appropriate to your use of constraints = none, or vice versa. Mark On Wed, Oct 22, 2014 at 4:26 AM, Kester Wong wrote: > Dear all, > > > I am intrigued by the error that I have received this morning, as follows: > > > > The charge group starting at atom 37920 moved more than the distance > allowed by the domain decomposition (1.40) in direction Y > > distance out of cell 7.144197 > > Old coordinates: 54.499 39.697 14.058 > > New coordinates: 54.499 39.697 14.058 > > Old cell boundaries in direction Y: 19.468 32.846 > > New cell boundaries in direction Y: 18.667 32.553 > > > If the charge group moved, if any, then shouldn't the new coordinates be > showing different values? > > It was a new NPT calculation that I continued from a 20ns NVT run, so it > should be equilibrated well enough, for a simple water on graphene system. > > > Using GROMACS 5.0, I was unable to start the NPT with Berendsen > thermostat, so I had to go with Parrinello-Rahman with a tau-P at 5.0 (my > tau-T was 0.5, following the general rule of thumb, that tau-P should be > larger than tau-T to allow thermal degrees of freedom to equilibrate faster > than the box size). > > > Should I reduce tau-P? > > > > > Below is my NPT.mdp parameters: > > ; RUN CONTROL PARAMETERS > > integrator = md > > tinit= 2.000 > > dt = 0.002; 2 fs > > nsteps = 500 ; 10,000 ps > > comm-mode= Linear > > nstcomm = 10 > > > emtol= 0.001 > > niter= 30 > > > ; OUTPUT CONTROL OPTIONS > > nstxout = 5000; save coordinates every 8 ps > > nstvout = 5000; save velocities every 8 ps > > nstfout = 0 > > nstlog = 5000; update log file every 8 ps > > nstenergy= 5000; save energies every 8 ps > > ;nstxtcout is replaced with nstxout-compressed > > nstxout-compressed = 5000; no. of steps between writing > coordinates using lossy compression > > ;xtc-precision is replaced with compressed-x-precision > > compressed-x-precision = 3000; precision with which to write to the > compressed trajectory file > > > ; Periodic boundary conditions: xyz (default), no (vacuum) > > cutoff-scheme= Verlet ; default for GROMACS-5.0 > > nstlist = 1 ; A smaller nstlist may reduce LINCS > warnings > > ns-type = grid ; > > pbc = xyz > > ;periodic_molecules = yes ; cannot be used with SHAKE > > ; nblist cut-off > > rlist= 1.40 ; short-range neighbourlist cutoff > > nstcalclr= 1 > > > coulombtype = PME > > coulomb-modifier = Potential-shift-Verlet > > r_coulomb= 1.40 ; short-range electrostatic cutoff > > rcoulomb-switch = 0 ; used when potential-switch > (coulomb-modifier) is specified > > epsilon-r= 1 ; default value=1 > > pme_order= 4 > > fourierspacing = 0.12 > > fourier_nx = 0 > > fourier_ny = 0 > > fourier_nz = 0 > > ewald_rtol = 1e-05 > > ewald_geometry = 3d > > epsilon_surface = 0 ; Use 0 when simulation is done with PME > > > > ;vdw-type = switch is replaced with the following two flags in GROMACS-5.0 > > vdwtype = Cut-off > > vdw_modifier = Potential-switch > > ; cut-off lengths > > rvdw-switch = 1.00 > rvdw = 1.40 ; short-range van der Waals cutoff > > constraints = none > constraint-algorithm = SHAKE > continuation = yes; starting from NVT run > Shake-SOR= no > shake-tol= 0.0001 > ;lincs-order = 4 ; accuracy of LINCS > ;lincs-iter = 24; also related to accuracy > ; Lincs will write a warning to the stderr if in one step a bond > ; rotates over more degrees than > ;lincs-warnangle = 30 > > Tcoupl = v-rescale > nh-chain-length = 1; the leapfrog md integrator only supports > 1 > ; Groups to couple separately > tc-grps = GRA SOL > ; Time constant (ps) and reference temperature (K) > tau-t= 0.5 0.5 > ref-t= 300 300 > nsttcouple = 20 ; added by k-wong ; not specified in > Yanbin's MDP > > Pcoupl = Parrinello-Rahman > Pcoupltype = isotropic > ; Time constant (ps), compressibility (1/bar) and reference P (bar) > tau-p= 5.0 ; time constant in ps > compressibility = 4.5e-5 ; isothermal compressibility of water, > bar^-1 > ref-p= 1.0 ; reference pressure, in bar > > > ; Non-equilibrium MD stuff > freezegrps
Re: [gmx-users] it is very slowly to run gromacs with OpenMPI
On Wed, Oct 22, 2014 at 4:08 AM, Vinson Leung wrote: > Hi all. I rencently I try different MPI library to run gromacs and find > that unlike Intel MPI and MPICH (which is normally can reach nearly 100% > CPU utilization ), it only can reach 20% CPU utilization when using > OpenMPI. It seriously contradict the offical Performance checklist ( > http://www.gromacs.org/Documentation/Performance_checklist) which claims > that OpenMPI usually has good performance and causes little trouble :( > What were your performance observations on another MPI program? I'll bet the OpenMPI back end is not configured suitably for your hardware. Mark And I also got some message when I run with OpenMPI: > > [cn3:28072] 9 more processes have sent help message > help-opal-shmem-mmap.txt / mmap on nfs > [cn3:28072] Set MCA parameter "orte_base_help_aggregate" to 0 to see all > help / error messages > > Any idea? > Thanks > > VIncent > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Segmentation fault while diagonalizing covariance matrix using g_covar
On Tue, Oct 21, 2014 at 11:46 PM, Mendez Giraldez, Raul <
rmen...@email.unc.edu> wrote:
> Dear gmx users,
>
> I am computing PCA on a system with 15476 atoms (a matrix of 46428x46428),
> using g_covar. The covariance matrix seems to be built, however it crashes
> few hours later after diagonalization takes place:
>
> Calculating the average structure ...
> trn version: GMX_trn_file (single precision)
> Reading frame 5 time 60250.000
> Reading frame 12 time 60650.000
> Readin
> Reading frame 70 time 63000.000
> Reading frame 130 time 66500.000
> Reading frame 190 time 69500.000
> Reading frame 800 time 1.000
> Last frame800 time 10.000
>
> Back Off! I just backed up average.pdb to ./#average.pdb.2#
> Constructing covariance matrix (46428x46428) ...
> Reading frame 5 time 60250.000
> Reading frame 12 time 60650.000
> Readin
> Reading frame 70 time 63000.000
> Reading frame 130 time 66500.000
> Reading frame 190 time 69500.000
> Reading frame 800 time 1.000
> Last frame800 time 10.000
> Read 801 frames
>
> Trace of the covariance matrix: 1.87421e+06 (u nm^2)
>
> Diagonalizing ...
> /nas02/home/r/m/rmendez/Work/Scripts/Essential_Dynamics_protein_ions.sh:
> line 8: 1013 Segmentation fault (core dumped)
> g_covar -s ${id}_${tag_gro}.gro -f ${id}_${tag_trr}.trr -v
> ${id}_protein_ions_eigenvector.trr -mwa -o ${id}_protein_ions_ED
> -n ${id}_${tag_trr}.protein_ions.ndx <
> ~/Work/Data/RyR/g_covar_proteins_ions
>
>
> You probably would say it is a memory problem, however I am booking 800 Gb
> of RAM, and when I check the memory usage, it does not seem to go further
> than 16 Gb:
>
I'd say that's a suspiciously round number that might be the limit on the
actual virtual memory available, but you'll have to ask your cluster admins
about that.
> Accounting information about jobs that are:
> - submitted by all users.
> - accounted on all projects.
> - completed normally or exited
> - executed on all hosts.
> - submitted to all queues.
> - accounted on all service classes.
>
> --
>
> Job <704235>, User , Project ,
> Application efault>, Status , Queue , Command
>
> me/r/m/rmendez/Work/Scripts/Essential_Dynamics_protein_ion
> s.sh g4934v 100ns.last_4
> helical_restraints.extended>,
> Share group charged
> Mon Oct 20 13:16:17: Submitted from host , CWD
> ez/Work/g4934v>, Output File
> t>, Error File ;
> Mon Oct 20 13:16:22: Dispatched 1 Task(s) on Host(s) , Allocated
> 1 Sl
> ot(s) on Host(s) , Effective RES_REQ
> ( hca_ready) && type == any))] order[mem]
> rusage[mem=800.0
> 0] same[model] >;
> Tue Oct 21 04:35:44: Completed .
>
> Accounting information about this job:
> Share group charged
> CPU_T WAIT TURNAROUND STATUS HOG_FACTORMEMSWAP
> 55002.445 55167 exit 0.997016G 16G
>
> --
>
> SUMMARY: ( time unit: second )
> Total number of done jobs: 0 Total number of exited jobs: 1
> Total CPU time consumed: 55002.4 Average CPU time consumed: 55002.4
> Maximum CPU time of a job: 55002.4 Minimum CPU time of a job: 55002.4
> Total wait time in queues: 5.0
> Average wait time in queue:5.0
> Maximum wait time in queue:5.0 Minimum wait time in queue:5.0
> Average turnaround time: 55167 (seconds/job)
> Maximum turnaround time: 55167 Minimum turnaround time: 55167
> Average hog factor of a job: 1.00 ( cpu time / turnaround time )
> Maximum hog factor of a job: 1.00 Minimum hog factor of a job: 1.00
> Total Run time consumed: 55162 Average Run time consumed: 55162
> Maximum Run time of a job: 55162 Minimum Run time of a job: 55162
>
> Does anyone know why g_covar crashes and/or what is the expected memory
> usage for a 46428x46428 matrix ?
>
Likely, it's not able to get enough memory. No. You should be thinking
seriously about whether you can do a sensible analysis on all those degrees
of freedom. You can construct a memory estimate by observing the
requirements for g_covar on various subsets of your system (e.g. alpha C,
then backbone atoms).
Mark
> Thank you so much in advance,
>
> Raul
>
> Raul Mendez Giraldez, PhD
> Dokholyan Lab
> Dept. Biophysics & Biochemistry
> Genetic Medicine
> University of North Carolina
> 120 Mason Farm Road
> Chapel Hill, NC 27599
> US
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
Re: [gmx-users] charge group moved too far between two domain decomposition step
On Wed, Oct 22, 2014 at 6:37 AM, Kester Wong wrote: > Hi Mark, > > > Thanks for the input, I thought a time step of 2 fs is small enough? > Not always for unconstrained bonds. The largest stable time step is determined by the size of the period of the fastest oscillation, which is vibrations of bonds to hydrogen. 2fs stretches the friendship there, and you would certainly want to equilibrate thoroughly at a smaller time step if you are doing messy things like freezing nanotubes and using pressure coupling (which would not be my go-to method without a clear demonstration that it produces valid results). More generally, equilibration of a not-quite-right structure works better with a smaller timestep, because that copes better with the artificially large forces you get... > Should I change my constraint to constraints = h-bonds instead? > That would be normal. > Or, > > > Should I use: > > dt = 0.001; 1 fs > > constraints = none > > constraint-algorithm = shake > Plausible, but you want to run the final simulation with constraints for the higher ns/day you obtain... Mark Cheers, > > Kester > > > You should start by using a time step more appropriate to your use of > constraints = none, or vice versa. > > Mark > > On Wed, Oct 22, 2014 at 4:26 AM, Kester Wong wrote: > > > Dear all, > > > > > > I am intrigued by the error that I have received this morning, as follows: > > > > > > > > The charge group starting at atom 37920 moved more than the distance > > allowed by the domain decomposition (1.40) in direction Y > > > > distance out of cell 7.144197 > > > > Old coordinates: 54.499 39.697 14.058 > > > > New coordinates: 54.499 39.697 14.058 > > > > Old cell boundaries in direction Y: 19.468 32.846 > > > > New cell boundaries in direction Y: 18.667 32.553 > > > > > > If the charge group moved, if any, then shouldn't the new coordinates be > > showing different values? > > > > It was a new NPT calculation that I continued from a 20ns NVT run, so it > > should be equilibrated well enough, for a simple water on graphene system. > > > > > > Using GROMACS 5.0, I was unable to start the NPT with Berendsen > > thermostat, so I had to go with Parrinello-Rahman with a tau-P at 5.0 (my > > tau-T was 0.5, following the general rule of thumb, that tau-P should be > > larger than tau-T to allow thermal degrees of freedom to equilibrate faster > > than the box size). > > > > > > Should I reduce tau-P? > > > > > > > > > > Below is my NPT.mdp parameters: > > > > ; RUN CONTROL PARAMETERS > > > > integrator = md > > > > tinit= 2.000 > > > > dt = 0.002; 2 fs > > > > nsteps = 500 ; 10,000 ps > > > > comm-mode= Linear > > > > nstcomm = 10 > > > > > > emtol= 0.001 > > > > niter= 30 > > > > > > ; OUTPUT CONTROL OPTIONS > > > > nstxout = 5000; save coordinates every 8 ps > > > > nstvout = 5000; save velocities every 8 ps > > > > nstfout = 0 > > > > nstlog = 5000; update log file every 8 ps > > > > nstenergy= 5000; save energies every 8 ps > > > > ;nstxtcout is replaced with nstxout-compressed > > > > nstxout-compressed = 5000; no. of steps between writing > > coordinates using lossy compression > > > > ;xtc-precision is replaced with compressed-x-precision > > > > compressed-x-precision = 3000; precision with which to write to the > > compressed trajectory file > > > > > > ; Periodic boundary conditions: xyz (default), no (vacuum) > > > > cutoff-scheme= Verlet ; default for GROMACS-5.0 > > > > nstlist = 1 ; A smaller nstlist may reduce LINCS > > warnings > > > > ns-type = grid ; > > > > pbc = xyz > > > > ;periodic_molecules = yes ; cannot be used with SHAKE > > > > ; nblist cut-off > > > > rlist= 1.40 ; short-range neighbourlist cutoff > > > > nstcalclr= 1 > > > > > > coulombtype = PME > > > > coulomb-modifier = Potential-shift-Verlet > > > > r_coulomb= 1.40 ; short-range electrostatic cutoff > > > > rcoulomb-switch = 0 ; used when potential-switch > > (coulomb-modifier) is specified > > > > epsilon-r= 1 ; default value=1 > > > > pme_order= 4 > > > > fourierspacing = 0.12 > > > > fourier_nx = 0 > > > > fourier_ny = 0 > > > > fourier_nz = 0 > > > > ewald_rtol = 1e-05 > > > > ewald_geometry = 3d > > > > epsilon_surface = 0 ; Use 0 when simulation is done with PME > > > > > > > > ;vdw-type = switch is replaced with the following two flags in GROMACS-5.0 > > > > vdwtype = Cut-off > > > > vdw_modifier = Pot
Re: [gmx-users] Implementation of SHAKE
Hi, No, it's the original, as cited in the manual. Mark On Wed, Oct 22, 2014 at 6:06 PM, Mario Fernández Pendás wrote: > Dear all, > > Am I right if I say that the SHAKE algorithm is implemented in GROMACS > following the ideas presented in "A fast SHAKE algorithm to solve distance > constraint equations for small molecules in molecular dynamics simulations" > by Kräutler,van Gunsteren and Hünenberger? > > > http://onlinelibrary.wiley.com/doi/10.1002/1096-987X%2820010415%2922:5%3C501::AID-JCC1021%3E3.0.CO;2-V/abstract > > Thank you very much. > > Cheers, > Mario Fernández-Pendás > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] error in the middle of running mdrun_mpi
Hi, The warning message told you not to increase the table distance unless you were sure the table distance was the problem. Why were you sure the table distance was the problem, rather than some form of general instability of your system? In addition to all the usual reasons for http://www.gromacs.org/Documentation/Terminology/Blowing_Up, the GB kernels are completely untested, so you might try running with 4.5.7 (last version known to be probably-good for GB) to see whether the problem is in the code or your setup. Mark On Thu, Oct 23, 2014 at 10:38 PM, Nizar Masbukhin wrote: > Dear gromacs users, > > I try simulate protein folding using REMD sampling method in implicit > solvent. I run my simulation on MPI-compiled gromacs 5.0.2 on single node. > I have succesfully minimized &equilibrated (NVT-constrained, and NPT > constrained) my system. However, In the middle of mdrun_mpi process, the > warning messages appear. > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > *starting mdrun 'Protein'5 steps, 50.0 ps.starting mdrun > 'Protein'5 steps, 50.0 ps.starting mdrun 'Protein'5 > steps, 50.0 ps.starting mdrun 'Protein'5 steps, 50.0 > ps.starting mdrun 'Protein'starting mdrun 'Protein'5 steps, > 50.0 ps.starting mdrun 'Protein'5 steps, 50.0 ps.starting > mdrun 'Protein'5 steps, 50.0 ps.5 steps, 50.0 > ps.step 2873100, will finish Sat Nov 1 10:03:07 2014WARNING: Listed > nonbonded interaction between particles 192 and 197at distance 16.773 which > is larger than the table limit 10.500 nm.This is likely either a 1,4 > interaction, or a listed interaction insidea smaller molecule you are > decoupling during a free energy calculation.Since interactions at distances > beyond the table cannot be computed,they are skipped until they are inside > the table limit again. You willonly see this message once, even if it > occurs for several interactions.IMPORTANT: This should not happen in a > stable simulation, so there isprobably something wrong with your system. > Only change the table-extensiondistance in the mdp file if you are really > sure that is the reason.* > > > > > > > > > > > > > > > > > > > > > *[nizarPC:07548] *** Process received signal ***[nizarPC:07548] Signal: > Segmentation fault (11)[nizarPC:07548] Signal code: Address not mapped > (1)[nizarPC:07548] Failing at address: 0x1ef8d90[nizarPC:07548] [ 0] > /lib/x86_64-linux-gnu/libc.so.6(+0x36c30) [0x7f610bc9fc30][nizarPC:07548] [ > 1] > > /usr/local/gromacs/bin/../lib/libgromacs_mpi.so.0(nb_kernel_ElecGB_VdwLJ_GeomP1P1_F_avx_256_single+0x836) > [0x7f610d3a2466][nizarPC:07548] [ 2] > /usr/local/gromacs/bin/../lib/libgromacs_mpi.so.0(do_nonbonded+0x240) > [0x7f610d235a30][nizarPC:07548] [ 3] > /usr/local/gromacs/bin/../lib/libgromacs_mpi.so.0(do_force_lowlevel+0x1d3e) > [0x7f610d97bebe][nizarPC:07548] [ 4] > > /usr/local/gromacs/bin/../lib/libgromacs_mpi.so.0(do_force_cutsGROUP+0x1510) > [0x7f610d91bbe0][nizarPC:07548] [ 5] mdrun_mpi(do_md+0x57c1) > [0x42e5e1][nizarPC:07548] [ 6] mdrun_mpi(mdrunner+0x12a1) > [0x413af1][nizarPC:07548] [ 7] mdrun_mpi(_Z9gmx_mdruniPPc+0x18e5) > [0x4337b5][nizarPC:07548] [ 8] > > /usr/local/gromacs/bin/../lib/libgromacs_mpi.so.0(_ZN3gmx24CommandLineModuleManager3runEiPPc+0x92) > [0x7f610ce15a42][nizarPC:07548] [ 9] mdrun_mpi(main+0x7c) > [0x40cb8c][nizarPC:07548] [10] > /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf5) > [0x7f610bc8aec5][nizarPC:07548] [11] mdrun_mpi() [0x40ccce][nizarPC:07548] > *** End of error message > > ***--mpirun > noticed that process rank 5 with PID 7548 on node nizarPC exited on signal > 11 (Segmentation fault).* > I have increased the table-extension to 500.00 (how much this value should > be?), and re-grompp and mdrun again. there were no warning message > regarding table-extension anymore, However, this error messages showed: > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > *starting mdrun 'Protein'5 steps, 50.0 ps.starting mdrun > 'Protein'5 steps, 50.0 ps.starting mdrun 'Protein'5 > steps, 50.0 ps.starting mdrun 'Protein'5 steps, 50.0 > ps.starting mdrun 'Protein'5 steps, 50.0 ps.starting mdrun > 'Protein'starting mdrun 'Protein'5 steps, 50.0 ps.starting > mdrun 'Protein'5 steps, 50.0 ps.5 steps, 50.0 > ps.step 4142800, will finish Sat Nov 1 10:35:55 2014[nizarPC:09984] *** > Process received signal ***[nizarPC:09984] Signal: Segmentation fault > (11)[nizarPC:09984] Signal code: Address not mapped (1)[nizarPC:09984] > Failing at address: 0x1464040[nizarPC:09984] [ 0] > /lib/x86_64-linux-gnu/libc.so.6(+0x36c30) [0x7fa764b65c30][nizarPC:09984] [ > 1] > > /usr/local/gromacs/bin/../lib/libgromacs_mpi.so.0(nb_kernel_ElecGB_VdwLJ_GeomP1P1_F_avx_256_single+0x85f) > [0x7fa76626848f][nizarPC:09984] [
Re: [gmx-users] Simulating Multiple Solute Particles
On Sat, Oct 25, 2014 at 7:23 AM, Nathan K Houtz wrote: > Hello, I apologize for any ignorance but I'm quite new to gromacs and am > confused about a few things. > > I want to run some simulations of a small molecule, tetrolic acid > (CH3-C≡C-COOH) dissolved in a box of water. I'm doing this to see if a > united atom approximation on the methyl group is sufficiently good for > saving a bit of computation time. I have created a .gro file and a .top > file and attempted to put it into gromacs but I don't know how to model > more than one molecule of TTA. All of the tutorials I've looked up involve > solvating enormous proteins and they only do one at a time. I'd like to > simulate hundreds of TTA molecules with an appropriate amount of water > molecules. I attempted to do this by specifying the numbers of TTA and H2O > in my topology file, but when I tried to solvate it, gromacs removed the > line specifying how many waters and replaced it with its own number (216) > and made the box way too small to fit any more TTA. I feel like this may be > trivial, but I'm stuck. I really appreciate anyone's help. > You can adapt http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents to do this. > After I figure this out, I'm going to try do dissolve tetrolic acid in > chloroform, then ethanol as well. I suspect gromacs doesn't have a built in > .gro or .top files for either of those (certainly not chloroform). Would > the solvate command work just as well if I created my own? > Yes, but perhaps gmx solvate -p won't quite do what you want. Do equilbrate that box decently; garbage in -> garbage out. Mark > Thanks in advance! > N.H. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Cannot combine residue position based cog selection with index output for g_select
Hi, I'm not the expert here, but I think that gmx select -selrpos has options that you should be able to use here. See gmx help selections positions Mark On Fri, Oct 24, 2014 at 10:43 PM, Huang Dongxu wrote: > Hi, > > I have a system consists of a box of water and a monolayer of polymer in > the center. I am trying to extract solvent molecules that have z > coordinates greater than 5 nm using g_select and output an index file. > Basically I want to separate my system into two portions: a box of waters > above the monolayer and the rest of the system containing the monolayer. > With the water only portion extracted by trajconv, I want to use genion to > replace some water molecules with salt and put this modified portion back > to my system that contains the monolayer. > > Right now, I am able to use g_select -on -select "resname SOL and z>5" to > select all atoms that belong to SOL and has z > 5 nm. However, this way > does not guarantee that all the atoms selected are from SOL molecules whose > cog are above z=5 plane. And as a result, some atoms that are part of SOL > molecules below the z=5 plane are also selected and the entire selection > contains some complete water molecules and some atoms that are from below > plane water molecules (incomplete waters). > > I am not sure with this kind of selection, if I extract it with trajconv, > and replace water with salt by genion, and then put it back to original > system, will I get correct alignment of those atoms from incomplete water > molecules and get the desired configuration. ( I think genion will only > replace complete residue; however, when using trajconv to generate new > coordination files, I am not sure if the system will be re-set to origin or > not. If so then the coordinates will definitely be misplaced and when I put > the modified part back there will be misalignment). > > TO AVOID all that, I'd like to use "cog of SELECTION" option in the > g_select, except for 1 problems: the -on option only works with atom > selection. > > So my essential question is: is there a way to use g_select with both the > -on option and cog option? Or is there another way to finish my task? > > I have searched the archive and did not find something that answers my > question. > > Thank you all for helping out. > > Best, > > Dongxu Huang > Graduate student at Northwestern University > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] trjconv gets stuck on frame
Hi, The output does drop in frequency at some point, so that might be all you are seeing. Experiment with -b and values around the putative problem area. Mark On Oct 26, 2014 6:59 PM, "Eric Smoll" wrote: > Hello Gromacs users, > > I have a trajectory file script18_o.trr that I am trying to process. Using > gmxcheck, this file appears to be complete. When I execute the command > below > > trjconv -f ../script18/script18_o.trr -s ../script17/script17_o.tpr -o > tmp1.trr -pbc whole << EOF > 0 > EOF > > the code moves quickly through the first few hundred frames only to > consistently get stuck on frame 300... > > trn version: GMX_trn_file (single precision) > -> frame320 time 128.000-> frame300 time 120.000 > > How do I troubleshoot the problem? > > -Eric > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] how to make statistics?
Hi, What does gmx hbond -h suggest to you? Mark On Oct 26, 2014 5:16 PM, "Albert" wrote: > Hello: > > I am going to make statistics for how much percentage H-bond formed for > residue A and B. I am just wondering how can we to do this? > > thank you very much. > > Albert > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] trjconv gets stuck on frame
On Sun, Oct 26, 2014 at 11:44 PM, Eric Smoll wrote: > Hi Mark, > > Thank you for responding so rapidly. I should note that identical > processing (I use a script) on the trajectories produced by slightly > different chemical systems had no problem and trajconv produced a complete > processed trajectory. > > However, when processing the problematic few with trajconv, the trajectory > that is output is incomplete (the trjconv output has fewer frames than the > input trajectory). > > This is definitely not problem with the change in output frequency of > progress reports to the terminal. > > I am not sure if the -b flag is telling me anything. I move it around and > it still seems to get stuck. I have ~30,000 atoms in my system. The first > 120 ps are processed in ~ 5 seconds. The next 4 ps take ~ 30 sec. My > trajectory is many nanoseconds long. > The point is to try to see whether the issue happens x steps into the trajectory, or only at around t=120ps. Does it happen if you are using -pbc somethingelse? Does it happen if you copy the file to some other filesystem before using -pbc whole? One needs to find a pattern before one can guess where the problem might lie. > Again, my other chemically similar systems do no hang like this and the > simulation procedure is scripted so it is consistent across my different > chemical systems. > OK. It's possible your simulation system is doing something pathological in that trajectory, which somehow does not agree with the implementation of -pbc whole (I'm guessing wildly here), but one would need to try the above kinds of experiments to probe that, and or visualize the trajectory in some viewing program. Mark I am using gromacs/4.6.5. > > Best, > Eric > > On Sun, Oct 26, 2014 at 5:21 PM, Mark Abraham > wrote: > > > Hi, > > > > The output does drop in frequency at some point, so that might be all you > > are seeing. Experiment with -b and values around the putative problem > area. > > > > Mark > > On Oct 26, 2014 6:59 PM, "Eric Smoll" wrote: > > > > > Hello Gromacs users, > > > > > > I have a trajectory file script18_o.trr that I am trying to process. > > Using > > > gmxcheck, this file appears to be complete. When I execute the command > > > below > > > > > > trjconv -f ../script18/script18_o.trr -s ../script17/script17_o.tpr -o > > > tmp1.trr -pbc whole << EOF > > > 0 > > > EOF > > > > > > the code moves quickly through the first few hundred frames only to > > > consistently get stuck on frame 300... > > > > > > trn version: GMX_trn_file (single precision) > > > -> frame320 time 128.000-> frame300 time 120.000 > > > > > > How do I troubleshoot the problem? > > > > > > -Eric > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > posting! > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > * For (un)subscribe requests visit > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > > send a mail to gmx-users-requ...@gromacs.org. > > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] trjconv gets stuck on frame
Hi, Parallel file systems do give uneven service (e.g. one file has a chunk that lives somewhere that was under high load right when you asked for it...), so given that you can read the files normally on a normal filesystem, then you should double-check Stampede's user guides for how to make best use of their file systems, and/or take up the issue further with the admins there. Cheers, Mark On Mon, Oct 27, 2014 at 11:40 AM, Eric Smoll wrote: > Hi Mark, > > i understand. It wasn't getting stuck in one place, if I skip over the > problem time when executed from the beginning the slowdown still occurs. > > I am working on the Stampede Supercomputer using their install of gromacs > and for reasons I do not understand, this extremely slow processing only > occurs for some trajectories on Stampede. Thinking there was some problem > with the login nodes, I tried this on a compute node with the same results > - slow processing. > > I transferred my trajectory to my laptop, installed the same version of > gromacs, and processed it with trjconv at a reasonable speed. > > Best, > Eric > > > On Mon, Oct 27, 2014 at 5:33 AM, Mark Abraham > wrote: > > > On Sun, Oct 26, 2014 at 11:44 PM, Eric Smoll > wrote: > > > > > Hi Mark, > > > > > > Thank you for responding so rapidly. I should note that identical > > > processing (I use a script) on the trajectories produced by slightly > > > different chemical systems had no problem and trajconv produced a > > complete > > > processed trajectory. > > > > > > However, when processing the problematic few with trajconv, the > > trajectory > > > that is output is incomplete (the trjconv output has fewer frames than > > the > > > input trajectory). > > > > > > This is definitely not problem with the change in output frequency of > > > progress reports to the terminal. > > > > > > I am not sure if the -b flag is telling me anything. I move it around > and > > > it still seems to get stuck. I have ~30,000 atoms in my system. The > first > > > 120 ps are processed in ~ 5 seconds. The next 4 ps take ~ 30 sec. My > > > trajectory is many nanoseconds long. > > > > > > > The point is to try to see whether the issue happens x steps into the > > trajectory, or only at around t=120ps. Does it happen if you are using > -pbc > > somethingelse? Does it happen if you copy the file to some other > filesystem > > before using -pbc whole? One needs to find a pattern before one can guess > > where the problem might lie. > > > > > > > Again, my other chemically similar systems do no hang like this and the > > > simulation procedure is scripted so it is consistent across my > different > > > chemical systems. > > > > > > > OK. It's possible your simulation system is doing something pathological > in > > that trajectory, which somehow does not agree with the implementation of > > -pbc whole (I'm guessing wildly here), but one would need to try the > above > > kinds of experiments to probe that, and or visualize the trajectory in > some > > viewing program. > > > > Mark > > > > I am using gromacs/4.6.5. > > > > > > Best, > > > Eric > > > > > > On Sun, Oct 26, 2014 at 5:21 PM, Mark Abraham < > mark.j.abra...@gmail.com> > > > wrote: > > > > > > > Hi, > > > > > > > > The output does drop in frequency at some point, so that might be all > > you > > > > are seeing. Experiment with -b and values around the putative problem > > > area. > > > > > > > > Mark > > > > On Oct 26, 2014 6:59 PM, "Eric Smoll" wrote: > > > > > > > > > Hello Gromacs users, > > > > > > > > > > I have a trajectory file script18_o.trr that I am trying to > process. > > > > Using > > > > > gmxcheck, this file appears to be complete. When I execute the > > command > > > > > below > > > > > > > > > > trjconv -f ../script18/script18_o.trr -s ../script17/script17_o.tpr > > -o > > > > > tmp1.trr -pbc whole << EOF > > > > > 0 > > > > > EOF > > > > > > > > > > the code moves quickly through the first few hundred frames only to > > > > > consistently get stuck on frame 300... > > > > > > > > > > trn version: GMX_trn_file (single precision) > &
Re: [gmx-users] error in the middle of running mdrun_mpi
On Mon, Oct 27, 2014 at 6:05 PM, Nizar Masbukhin wrote: > i dont really understand the point. could you please what do you mean in > the last reply? > what command should i use? > > if, say i have 72 cores in 9 nodes, and 16 replicas to simulate in implicit > solvent. Hi, You can only use two MPI ranks per replica if there's a limit of two ranks per simulation. So that's 32 ranks total. So something like mpirun -np 32 mdrun_mpi -multidir -repl_ex whatever after setting up the MPI environment to fill four nodes. Mark -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Calculating intermolecular energies of water
On Tue, Oct 28, 2014 at 6:27 PM, David van der Spoel wrote: > On 2014-10-28 18:12, Jackson Chief Elk wrote: > >> Hi, >> When using g_energy to calculate short-range Coulomb interactions between >> a dynamically sized group of water, made with g_select, does the output >> contain both bonded and non bonded contributions? >> Jackson >> >> I don't think this is possible at all. You need to define energy groups > before your simulation. Indeed. But if Jackson meant to ask about short-range Coulomb, then bonded contributions do not apply. Nor would they if the water model was rigid, as is typically the case. Mark > > > -- > David van der Spoel, Ph.D., Professor of Biology > Dept. of Cell & Molec. Biol., Uppsala University. > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. > sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] The last line in a .gro file
Probably. Try a differently sized molecule ;-) Mark On Tue, Oct 28, 2014 at 5:58 PM, Agnivo Gosai wrote: > Dear Users > > The last line of the .gro file lists out three co-ordinates and the GROMACS > manual says that these are the box vectors : v1(x) , v2(y) and v3(z) > Now , before using editconf to place our molecule inside a box , there is > no box associated with the system. > But pdb2gmx generates this .gro file having the vectors listed in the last > line. > > My question is :- Is the last line has to do anything with the "size" of > the molecule ? > > Thanks & Regards > Agnivo Gosai > Grad Student, Iowa State University. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] force-switch as vdv-modifier
Hi, This is implemented only in Gromacs 5 Mark On Wed, Oct 29, 2014 at 8:06 AM, Chandan Choudhury wrote: > Dear gmx users, > > I was trying to use the Force-Switch as the vdv-modifier with Verlet cutoff > scheme. > The use of Force-Switch produces the following error: > > > > > > > *ERROR 1 [file grompp.mdp, line 63]: Invalid enum 'force-switch' for > variable vdw-modifier, using 'Potential-shift-Verlet' Next time use one > of: 'Potential-shift-Verlet' 'Potential-shift' 'None' 'Potential-switch' > 'Exact-cutoff'* > I am using the 4.6.6 version of GPU enabled gromacs. > > Please let me know how do I circumvent the error. > > The snippet of the mdp file is here: > > ; NEIGHBOR SEARCHING > cutoff-scheme= Verlet > nstlist = 10 > ns_type = grid > pbc = xyz > > ; Method for doing Van der Waals > vdw-modifier = force-switch > ; cut-off lengths > rvdw_switch = 1.1 > rvdw = 1.3 > > > > Thanks > Chandan > -- > Chandan Kumar Choudhury > National Chemical Laboratory, Pune > India > > *"All work and no play makes Jack a dull boy...”* > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] pdb2gmx
Hi, The .rtp files are used by pdb2gmx in order to recognize residues in the face of what can be massive noise in the input file. It primarily matches names of atoms and residues. It writes a coordinate and topology file whose atom and residue ordering matches each other, and whose atom types will permit parameter lookup from the force field data bases - atom and residues names become fairly (completely? idk) unimportant at this stage. I imagine it is possible to duplicate the same atom name within a residue for use with grompp, but likely there's no tool that generates such input for grompp, because they need unique atom names so they can bring order from chaos. Please check out the instructions and examples in Chapter 5 of the manual. Mark On Wed, Oct 29, 2014 at 1:11 AM, Eric Smoll wrote: > Hello Gromacs users, > > I would like to add a molecule as a "residue" in the aminoacids.rtp file > and I have a few questions. > > As far as I understand, a residue in a gro file can multiple atoms with the > same "atom name." What links every atom in this residue to parameters in > the top [ atoms ] directive is the *order.* The gro file "atom names" must > match the top file atoms names but the mapping of parameters is done via > the order, correct? This allows atoms in a residue to have the same "atom > name" but be associated > with a different "atom type," "charge group," etc... > > Does an entry in a residue database (e.g., aminoacids.rtp) work the same > way? > The syntax is shown below. > > [ TEST ] > [ atoms ] > ; atom_nameatom_typeatom_chargecharge_group > > I have to specify the "atom name," force field "atom type," "atom charge," > and "charge group" for every atom in the "TEST" residue in order. The "atom > name" must match the "atom name" in the input coordinate file but the > mapping is applied by the entry order, correct? I do no need unique "atom > names," correct? > > Best, > Eric > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] force-switch as vdv-modifier
On Wed, Oct 29, 2014 at 1:20 PM, Justin Lemkul wrote: > > > On 10/29/14 7:23 AM, Chandan Choudhury wrote: > >> Thanks Mark >> >> Is the Potential-Switch Algorithm is implemented in gmx 466? >> When I used Potential-Switch, grompp does not produce any error. >> >> > Yes, it is implemented, otherwise you would get a fatal error. > You will also see mdrun's log file acknowledge that setting in the parameter dump it produces early in the run. Mark > -Justin > > > It is not documented in the manual. >> >> Chandan >> >> On Wed, Oct 29, 2014 at 3:16 PM, Mark Abraham >> wrote: >> >> Hi, >>> >>> This is implemented only in Gromacs 5 >>> >>> Mark >>> >>> On Wed, Oct 29, 2014 at 8:06 AM, Chandan Choudhury >>> wrote: >>> >>> Dear gmx users, >>>> >>>> I was trying to use the Force-Switch as the vdv-modifier with Verlet >>>> >>> cutoff >>> >>>> scheme. >>>> The use of Force-Switch produces the following error: >>>> >>>> >>>> >>>> >>>> >>>> >>>> *ERROR 1 [file grompp.mdp, line 63]: Invalid enum 'force-switch' for >>>> variable vdw-modifier, using 'Potential-shift-Verlet' Next time use >>>> one >>>> of: 'Potential-shift-Verlet' 'Potential-shift' 'None' >>>> 'Potential-switch' >>>> 'Exact-cutoff'* >>>> I am using the 4.6.6 version of GPU enabled gromacs. >>>> >>>> Please let me know how do I circumvent the error. >>>> >>>> The snippet of the mdp file is here: >>>> >>>> ; NEIGHBOR SEARCHING >>>> cutoff-scheme= Verlet >>>> nstlist = 10 >>>> ns_type = grid >>>> pbc = xyz >>>> >>>> ; Method for doing Van der Waals >>>> vdw-modifier = force-switch >>>> ; cut-off lengths >>>> rvdw_switch = 1.1 >>>> rvdw = 1.3 >>>> >>>> >>>> >>>> Thanks >>>> Chandan >>>> -- >>>> Chandan Kumar Choudhury >>>> National Chemical Laboratory, Pune >>>> India >>>> >>>> *"All work and no play makes Jack a dull boy...”* >>>> -- >>>> Gromacs Users mailing list >>>> >>>> * Please search the archive at >>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>>> posting! >>>> >>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>> >>>> * For (un)subscribe requests visit >>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>>> send a mail to gmx-users-requ...@gromacs.org. >>>> >>>> -- >>> Gromacs Users mailing list >>> >>> * Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>> posting! >>> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> * For (un)subscribe requests visit >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>> send a mail to gmx-users-requ...@gromacs.org. >>> >>> >> >> >> > -- > == > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > == > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] SR and 14 terms for LJ and Coulomb interactions
On Thu, Oct 30, 2014 at 2:39 PM, Turgay Cakmak wrote: > Dear Gromacs Users, > > Thank you for your insightful comments. I am, however, still a bit confused > about the non-bonded terms in potential energy, so I would be happy if you > assisted me for a bit further. > > Is there any possible overlap between SR and 1-4 interactions? No, there is no double-counting. > In other > words, is it always true that > (please assume that long-range interactions are negligible). > Well, yes, but since the values of parameters are all coupled through the parameterization process, there isn't a true correspondence... 1-4 parameters are scaled in some force fields precisely because some component of those interactions is already described by dihedrals... > Similarly, does hold > in all possible cases? > Same applies. > In addition, vdW and Coulombic interactions are directional. Is a vector > addition necessary to get the total strength of these interactions, or does > only adding up the scalar values yield an accurate sum? > Potentials are scalar, forces are directional, magnitudes of forces are scalar. Be precise about what you mean, and the correct operation becomes clear :-) Mark For the record, I am simulating a fiber composed of several hundred peptide > molecules. > > Thank you for your time. > > Turgay > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Version 12
Mdrun reports its version, yes? Mark On Oct 31, 2014 7:14 AM, "lloyd riggs" wrote: > > Im getting a "Attempting to read a checkpoint file of version 15 with code > of version 12", does anyone know off hand which is version 12 ? Im guessing > lik 4.5.6 , but dont know. > > Stephan Watkins > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] mdrun error message in Computing Cluster
Hi, I've never seen that error. I hope you have a compelling scientific reason for installing such a slow old version :-) Mark On Oct 31, 2014 1:58 AM, "Agnivo Gosai" wrote: > Dear Users > > I compiled double precision Gromacs 4.5.6 in my university cluster ( named > CyEnce ). > It is the serial version as I did not compile mdrun separately as parallel > mdrun. > I followed the procedure in the below mentioned link :- > http://ringo.ams.sunysb.edu/index.php/Compiling_GROMACS_on_Cluster > But while using mdrun I am getting the following error :- > > Reading file em.tpr, VERSION 4.5.6 (double precision) > Starting 16 threads > tMPI Fatal error in pthreads.c, line 202: Failed to create POSIX > thread:Resource temporarily unavailable, rc=11 > Aborted > > I am not sure as to what this means. Any suggestions please ?? > > Thanks & Regards > Agnivo Gosai > Grad Student, Iowa State University. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Meaningless pressure values: NVT and NVE ensembles
Hi, Tiny systems will take a long time to show a converged value of pressure. See http://www.gromacs.org/Documentation/Terminology/Pressure. No observation of pressure in Gromacs is meaningful without mention of the length of post-equilibration measurement time and the error estimate gmx energy provides. Mark On Wed, Nov 5, 2014 at 12:46 PM, Francesco Mambretti < francesco.mambre...@studenti.unimi.it> wrote: > Thanks for the suggestion, but I fear it is not my case. > I obtain the same > meaningless results with version 5.0.2 installed > on another pc of my university. > I suspect it is something in Gromacs procedure > for computing pressures. > However, thanks > > Francesco > > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Meaningless pressure values: NVT and NVE ensembles
On Wed, Nov 5, 2014 at 1:17 PM, Francesco Mambretti < francesco.mambre...@studenti.unimi.it> wrote: > > So you confirm me that pressure calculation in Gromacs is done through > virial theorem and should provide meaningful results? > Yes, see manual section 3.4.3 > I start from a perfect fcc crystal and launch simulations of 20 ps...is it > a > too short simulation? density and temperature should be already optimized > for argon solid state. However, I am trying to run simulations of 2000 ps. > If the problem persists, I'll let you know. I can't imagine anything under a nanosecond being useful, and for a system that small, many nanoseconds is quite plausible. You should look at the graphs of pressure over time. Since you're generating velocities, you should be discarding the first fragment of your output. Mark > Thanks > > Francesco > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] md.log interpretation
Hi, I am not familiar with the implementation details, but I would assume there is a dependency on rcoulomb of the cost of the Born force chain rule. You can check this by trying different values. It might be faster to use infinite cutoffs (see manual) so that the algorithm does not need to search. Mark On Tue, Nov 4, 2014 at 1:34 AM, Nizar Masbukhin wrote: > Dear gromacs users, > I've just finished my NVT equilibration in implicit solvent. From md.log, i > see that most of time were used to calculate Forces (of Born force chain > rule). Could someone explain to me why calculating it takes so long? > > mdp setting: > > integrator=md > dt=0.004 > nstep=250 > bd-frict=50 > rlist=5 > rvdw=5 > rcoulomb=5 > nstlist=40 > implicit-solvent=GBSA > gb-alogarithm=still > nstgbradii=40 > gbradii=5 > gb-epsilon-solvent=80 > gb-salt-conc=0.2 > sa-algorithm=ace-approximation > sa-surface-tension=2.05 > constraints=all-bonds > constraints-algorithm=LINCS > lincs-order=12 > > > md.log > > M E G A - F L O P S A C C O U N T I N G > > NB=Group-cutoff nonbonded kernelsNxN=N-by-N cluster Verlet kernels > RF=Reaction-Field VdW=Van der Waals QSTab=quadratic-spline table > W3=SPC/TIP3p W4=TIP4p (single or pairs) > V&F=Potential and force V=Potential only F=Force only > > Computing: M-Number M-Flops % Flops > > - > NB VdW [V&F] 32677.013279 32677.013 0.0 > NB VdW [F] 1740991.575264 1740991.575 0.3 > NB VdW & Elec. [V&F] 1192677.312698 1192677.313 0.2 > NB VdW & Elec. [F] 106409048.599622 106409048.60017.9 > 1,4 nonbonded interactions 20035.628466 1803206.562 0.3 > Born radii (Still) 1999216.23274293963162.93915.8 > Born force chain rule 25548182.811729 *383222742.176* > 64.4 > NS-Pairs 64906.572700 1363038.027 0.2 > CG-CoM 205.506576 616.520 0.0 > Propers 15168.313980 3473543.901 0.6 > Impropers 637.980588 132699.962 0.0 > Pos. Restr. 3830.053530 191502.676 0.0 > Virial 82.6954711488.518 0.0 > Stop-CM 82.214752 822.148 0.0 > Calc-Ekin 822.011152 22194.301 0.0 > Lincs 4696.969329 281818.160 0.0 > Lincs-Mat 229529.791548 918119.166 0.2 > Constraint-V 9393.938658 75151.509 0.0 > Constraint-Vir 46.9739791127.375 0.0 > Virtual Site 3 615.868824 22787.146 0.0 > Virtual Site 3fd 791.205144 75164.489 0.0 > Virtual Site 3fad 168.761208 29701.973 0.0 > Virtual Site 3out 1893.632256 164746.006 0.0 > Virtual Site 4fdn 576.418152 146410.211 0.0 > (null) 476.315439 0.000 0.0 > > - > Total 595265438.267 100.0 > > - > > > R E A L C Y C L E A N D T I M E A C C O U N T I N G > > On 1 MPI rank > > Computing: Num Num CallWall time Giga-Cycles > Ranks Threads Count (s) total sum% > > - > Vsite constr. 111085001 96.421385.432 0.2 > Neighbor search11 27126 915.964 3661.462 2.1 > Force 111085001 *39317.742* 157168.118 > 91.3 > Vsite spread 111095852 142.563569.880 0.3 > Write traj.11 11030 425.764 1701.942 1.0 > Update 111085001 96.742386.714 0.2 > Constraints1110850011311.720 5243.449 3.0 > Rest 766.404 3063.612 1.8 > > - > Total 43073.320 172180.608 100.0 > > - > >Core t (s) Wall t (s)(%) >Time:41985.82843073.320 97.5 > 11h57:53 > (ns/day)(hour/ns) > Performance:
Re: [gmx-users] speed of 5.0.2 v.s 4.6
Yes, in general. Mark On Wed, Nov 5, 2014 at 5:11 PM, Johnny Lu wrote: > Hi. > > Do the two version of gromacs with mixed precision have similar speed? > > Thanks again. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Pressure Question
Hi, That's hard to say. You'd need to do multiple converged simulations at each set of conditions to know. First, make sure you've made a significant observation of the pressure. Mark On Tue, Nov 4, 2014 at 6:00 PM, Johnny Lu wrote: > Hi. > > If my NVT simulation of a protein in 30k molecules of water has a pressure > of 11 bar (error 0.5 bar from g_energy), will the dynamics (not > distribution of conformations) change enough that the mechanism inferred > from this simulation be significantly more unreliable than the mechanism > inferred from a 1 bar simulation? (Will the reviewers cut my paper into > ribbons?) > > Thanks again. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Fwd: Question about QM/MM calculations
Hi, Please ask such questions on the Gromacs users mailing list, where you have the best chance of reaching people who might know and help. Unfortunately, I have no experience with the QM/MM ports in Gromacs. I would be pleasantly surprised if any of them worked in versions subsequent to the one for which they were developed - they are not tested during development. Please get the Gromacs and Gaussian version appropriate to the time they were developed, and follow the instructions precisely. There may be useful knowledge if you search the mailing list archives. Mark -- Forwarded message -- From: Hooman Vahidi Date: Wed, Nov 5, 2014 at 6:00 PM Subject: Question about QM/MM calculations To: "mark.j.abra...@gmail.com" Dear Dr. Mark Abraham I am currently a student of chemistry in Mashhad University. I have been trying to perform QM/MM calculations by linking Gaussian03 source and Gromacs 4.6.5 for about four months, but I have not yet succeeded in doing so. My first problem is editing the four specific files of Gaussian (301, 510, 701, ), which you described in roadmap file. Since I have no experience in programming, I have no clue where exactly to perform specific editing in the code. Another problem is with makefile. In the guide, you have explained that for each edited file, one makefile should be compiled. Is makefile identical for all edited files? If not, then how to build these (make)files? Is it possible for you to send me edited versions of these four files (301, 510, 701, ), so that I could understand how they are edited? I kindly request you to help me out in this matter. I really appreciate your help and I am forever grateful. I am awaiting your response. Best wishes, Hooman -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Version problem
Hi, Well, you need to find out where you installed it (default /usr/local/bin). Using "which" or "locate" will only find the version from your OS distribution. Since you plan to use 5.0.2, you should uninstall the OS version using the package manager, to save yourself from further accidental confusion. Mark On Thu, Nov 6, 2014 at 12:43 PM, wrote: > > tried "which mdrun" > showing the path /usr/bin/mdrun, which v4.6.5, however I have downloaded > v5.0.2.tar.gz and used for installation. > > > > try to find mdrun program by typing this command on terminal: > > "which mdrun" > > will show path of mdrun program where it located. > > On Nov 6, 2014 4:01 PM, wrote: > > > >> Dear Dr. Carsten Kutzner, > >> I am unable to find the "gmx5/bin/GMXRC" in my machine, > >> used 'locate' and 'find' to search the location. > >> However I have source the following: > >> source /usr/share/gromacs/shell-specific/GMXRC.bashrc > >> Without this also mdrun is running. I am definitely missing something. > >> Kindly help. > >> > >> With best regards, > >> > >> Satya > >> > >> > On 06 Nov 2014, at 07:15, sa...@physics.iisc.ernet.in wrote: > >> > > >> >> Dear all, > >> >> I am new to GROMACS, just finish installation of v5.0.2, started > >> reading > >> >> online manual, as instructed executed the command: mdrun -version and > >> >> the > >> >> printout pasted below. > >> >> > >> >> It is printing GROMACS version 4.6.5, however I have installed > >> version > >> >> 5.0.2. What is the problem? > >> > Find the directory to where you have installed your GROMACS 5.0 > >> > executables > >> > and then do > >> > > >> > source /path/to/gmx5/bin/GMXRC > >> > > >> > which mdrun > >> > > >> > should now give you the 5.0 mdrun > >> > > >> > Carsten > >> > > >> >> > >> >> Regards, > >> >> Satyabrata Das > >> >> > >> >> > == > >> >> Program: mdrun > >> >> Gromacs version:VERSION 4.6.5 > >> >> Precision: single > >> >> Memory model: 64 bit > >> >> MPI library:thread_mpi > >> >> OpenMP support: enabled > >> >> GPU support:disabled > >> >> invsqrt routine:gmx_software_invsqrt(x) > >> >> CPU acceleration: SSE4.1 > >> >> FFT library:fftw-3.3.3-sse2-avx > >> >> Large file support: enabled > >> >> RDTSCP usage: enabled > >> >> Built on: Sun Dec 15 04:01:11 UTC 2013 > >> >> Built by: buildd@panlong [CMAKE] > >> >> Build OS/arch: Linux 3.2.0-37-generic x86_64 > >> >> Build CPU vendor: GenuineIntel > >> >> Build CPU brand:Intel(R) Xeon(R) CPU E5620 @ 2.40GHz > >> >> Build CPU family: 6 Model: 44 Stepping: 2 > >> >> Build CPU features: aes apic clfsh cmov cx8 cx16 htt lahf_lm mmx msr > >> >> nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 > >> >> sse4.1 > >> >> sse4.2 ssse3 > >> >> C compiler: /usr/bin/x86_64-linux-gnu-gcc GNU gcc-4.8.real > >> >> (Ubuntu/Linaro 4.8.2-10ubuntu1) 4.8.2 > >> >> C compiler flags: -msse4.1-Wextra > >> -Wno-missing-field-initializers > >> >> -Wno-sign-compare -Wall -Wno-unused -Wunused-value > >> -Wno-unused-parameter > >> >> -Wno-array-bounds -Wno-maybe-uninitialized -Wno-strict-overflow > >> >> -fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast -O3 > >> >> -DNDEBUG > >> >> satyabrata@satyabrata-desktop:~$ > >> >> > >> >> > >> >> > >> >> -- > >> >> This message has been scanned for viruses and > >> >> dangerous content by MailScanner, and is > >> >> believed to be clean. > >> >> > >> >> -- > >> >> Gromacs Users mailing list > >> >> > >> >> * Please search the archive at > >> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >> >> posting! > >> >> > >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> >> > >> >> * For (un)subscribe requests visit > >> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or > >> >> send a mail to gmx-users-requ...@gromacs.org. > >> > > >> > > >> > -- > >> > Dr. Carsten Kutzner > >> > Max Planck Institute for Biophysical Chemistry > >> > Theoretical and Computational Biophysics > >> > Am Fassberg 11, 37077 Goettingen, Germany > >> > Tel. +49-551-2012313, Fax: +49-551-2012302 > >> > http://www.mpibpc.mpg.de/grubmueller/kutzner > >> > http://www.mpibpc.mpg.de/grubmueller/sppexa > >> > > >> > -- > >> > Gromacs Users mailing list > >> > > >> > * Please search the archive at > >> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >> > posting! > >> > > >> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > > >> > * For (un)subscribe requests visit > >> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >> send > >> > a mail to gmx-users-requ...@gromacs.org. > >> > > >> > -- > >> > This message has been scanned for viruses and > >> > dangerous content by MailScanner, and is > >> > believed to be clean. > >> > > >> > > >> > >> > >> > >> -- > >> This
Re: [gmx-users] Minimization is not running
This is because you are using 4.6.5 provided by your OS, and it has been compiled assuming SSE4.1, but your machine is so old it only runs SSE2. When you find your 5.0.2 install, it will be probably compiled for SSE2. Mark On Thu, Nov 6, 2014 at 12:52 PM, wrote: > Dear all, > > I am just new to GROMACS, tried to install v5.0.2, although isntallation > was successful, while running it is giving problem: > > I am just trying to do the lysozyme tutorial, however first energy > minimization is not running, mdrun stopped with: > > === > Reading file em.tpr, VERSION 4.6.5 (single precision) > Using 1 MPI thread > Using 2 OpenMP threads > Compiled acceleration: SSE4.1 (Gromacs could use SSE2 on this machine, > which is better) > > Back Off! I just backed up em.trr to ./#em.trr.1# > > Back Off! I just backed up em.edr to ./#em.edr.1# > Illegal instruction (core dumped) > > > I have attached log file which shows during installation compiler flag > SSE4.1 was used instead of SSE2, how to fix this? > > With best regards, > > Satyabrata Das > -- > This message has been scanned for viruses and > dangerous content by MailScanner, and is > believed to be clean. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] gmx covar (Version 5.x) segfaults with covariance matrices bigger than 1500x1500
Hi, IIRC some minor bugs were fixed, but a regression like that should be dealt with... please file at http://redmine.gromacs.org. Mark On Thu, Nov 6, 2014 at 12:00 PM, Machtens, Jan-Philipp < j.macht...@fz-juelich.de> wrote: > Dear all, > I observed that g_covar in Gromacs 5.0.2 segfaults at the diagonalization > step, if the group for the covariance analysis is bigger than 500 atoms, > i.e. if the covariance matrix is bigger than 1500x1500. > In my hands, this problem does not arise with g_covar 4.6.x. The results > obtained from g_covar (version 5.x) on groups <= 500 atoms that I obtained > were the same os those from version 4.6.x and also verified manually. > Memory is not the problem here. The problem is independent on single/double > precision. > > Before posting this on redmine.gromacs I first want to check whether > someone here has made a contradicting experience which would argue against > a possible bug introduced in 5.0.2? > Thanks. > Cheers, > Jan-Philipp Machtens > > > > > > > Forschungszentrum Juelich GmbH > 52425 Juelich > Sitz der Gesellschaft: Juelich > Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 > Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher > Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), > Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, > Prof. Dr. Sebastian M. Schmidt > > > > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Tested and most compatible Gromacs version for Mac OS Leopard (10.5)
Hi, In principle, any Gromacs version will work on any Mac OS version, but the problem lies in getting a compiler toolchain that works correctly. Stock Apple compilers are based on clang, which doesn't support OpenMP, and would be outperformed by gcc if the linker in the binutils supported AVX SIMD (which it doesn't). You can probably build your own gcc toolchain that works, but the most reliable path is to use the Intel compilers (which are not free). And it gets more fun if you want CUDA support. Mark On Thu, Nov 6, 2014 at 11:45 AM, PAVAN PAYGHAN wrote: > Dear Gromacs Users, > > Please suggest me latest gromacs version which will suit Mac OS Leopard (on > Apple cluster) without having any problems. > Can it be possible to use 5.0 Gromacs series for the same?. I searched in > net and mailing list didn't found any reliable answer. > Thanking You in advance. > > Pavan Payghan > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Pressure Question
On Thu, Nov 6, 2014 at 12:39 PM, Johnny Lu wrote: > I was not offended by the suggestion. With a sufficiently large number of > water molecules, the protein would behave in the same way, under all three > ensembles. > Barostat and thermostat are artificial in some way. Biochemistry takes place in the NPT ensemble... NVT and NPT are different from NVE, but that doesn't make them artificial. Implementing such algorithms correctly is more tricky, however. At least, even the > diffusion coefficient is different in a force field paper that used both > NVE and NVT. Langevin thermostat destroys some momentum transfer. > > This is my first paper, and I don't know if the reviewer will be fine if I > report that my simulation has an average pressure of 11 bar with error 0.5 > bar. That would concern me, slightly more than the fact that you have a single simulation upon which to draw conclusions. Average pressure > 1 in a fixed-volume ensemble means the system wants to change volume (get larger? I forget the convention). Why not do some NPT to find a volume it presumably likes better, and do another run? If the results are different, then you need more runs to find out what's going on. If the results are the same, then you've added weight to your conclusions. Mark On Thu, Nov 6, 2014 at 5:34 AM, Téletchéa Stéphane < > stephane.teletc...@univ-nantes.fr> wrote: > > > Le 06/11/2014 06:16, Antonio Baptista a écrit : > > > >> > >> In particular, the virial-based "instantaneous pressure" (call it P') > >> computed in simulations has its ensemble average equal to the > thermodynamic > >> pressure P (check any good book on molecular simulation). But, as others > >> already pointed out, this P' is well-known to show extremelly large > >> fluctuations, meaning that its average computed from the simulation has > >> usually a very large statistical spread. In other words, although the > >> ensemble average of P' is strictly equal to P, its simulation average > is a > >> random variable that often shows large deviations from P (especially for > >> short simulations). To get an idea of what is an acceptable error for > the > >> average of P', you may look at its distribution histogram in the NPT > >> simulation. > >> > > > > Dear Antonio, > > > > Sorry if my message sound "aggressive" when I talked about "totally > > irrevelevant", I will clarify my thoughts. > > > > From a theoretical point of view, you are right, each ensemble is > > accessible. > > > > From a biological point of view, though, the concept of fixing the volume > > is less reasonable: > > we live at constant pressure and temperature, and also at tighly > > controlled pH, and salt concentrations. > > > > The volume varies though, as you feel it when the weather is getting hot > > or cold. > > > > My point was exactly what your are telling in a more formal way than me: > > "this P' is well-known to show extremely large fluctuations" > > > > Well, digging a bit more on my "feeling", I also found opposite arguments > > on the AMBER mailing list, > > like here: http://archive.ambermd.org/201103/0431.html > > > > So I'll got back again on my research and adjust my "mind" on the actual > > bleeding edge simulations > > taking into account all the recent code and force fields progresses. > > > > Best, > > > > Stéphane > > > > -- > > Team Protein Design In Silico > > UFIP, UMR 6286 CNRS, > > UFR Sciences et Techniques, > > 2, rue de la Houssinière, Bât. 25, > > 44322 Nantes cedex 03, France > > Tél : +33 251 125 636 > > Fax : +33 251 125 632 > > http://www.ufip.univ-nantes.fr/ - http://www.steletch.org > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at http://www.gromacs.org/ > > Support/Mailing_Lists/GMX-Users_List before posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Pressure Question
Hi, Note that using the Berendsen thermostat in Gromacs adds defects for no gain, compared with the Bussi v-rescale thermostat. The latter *is* Berendsen, plus a stochastic term that produces the right energy and velocity distributions (unlike Berendsen). I'd give serious consideration to rejecting a paper that used Gromacs and the Berendsen thermostat, particularly if they did not discuss why the known defects of Berendsen were acceptable for their work. Mark On Thu, Nov 6, 2014 at 4:18 PM, Johnny Lu wrote: > That post in the amber mailing list was quite interesting. May be using a > weak berendsen thermostat in NVT is fine for them. Thanks for sharing that. > > On Thu, Nov 6, 2014 at 6:39 AM, Johnny Lu wrote: > > > I was not offended by the suggestion. With a sufficiently large number of > > water molecules, the protein would behave in the same way, under all > three > > ensembles. > > Barostat and thermostat are artificial in some way. At least, even the > > diffusion coefficient is different in a force field paper that used both > > NVE and NVT. Langevin thermostat destroys some momentum transfer. > > > > This is my first paper, and I don't know if the reviewer will be fine if > I > > report that my simulation has an average pressure of 11 bar with error > 0.5 > > bar. > > > > > > On Thu, Nov 6, 2014 at 5:34 AM, Téletchéa Stéphane < > > stephane.teletc...@univ-nantes.fr> wrote: > > > >> Le 06/11/2014 06:16, Antonio Baptista a écrit : > >> > >>> > >>> In particular, the virial-based "instantaneous pressure" (call it P') > >>> computed in simulations has its ensemble average equal to the > thermodynamic > >>> pressure P (check any good book on molecular simulation). But, as > others > >>> already pointed out, this P' is well-known to show extremelly large > >>> fluctuations, meaning that its average computed from the simulation has > >>> usually a very large statistical spread. In other words, although the > >>> ensemble average of P' is strictly equal to P, its simulation average > is a > >>> random variable that often shows large deviations from P (especially > for > >>> short simulations). To get an idea of what is an acceptable error for > the > >>> average of P', you may look at its distribution histogram in the NPT > >>> simulation. > >>> > >> > >> Dear Antonio, > >> > >> Sorry if my message sound "aggressive" when I talked about "totally > >> irrevelevant", I will clarify my thoughts. > >> > >> From a theoretical point of view, you are right, each ensemble is > >> accessible. > >> > >> From a biological point of view, though, the concept of fixing the > volume > >> is less reasonable: > >> we live at constant pressure and temperature, and also at tighly > >> controlled pH, and salt concentrations. > >> > >> The volume varies though, as you feel it when the weather is getting hot > >> or cold. > >> > >> My point was exactly what your are telling in a more formal way than me: > >> "this P' is well-known to show extremely large fluctuations" > >> > >> Well, digging a bit more on my "feeling", I also found opposite > arguments > >> on the AMBER mailing list, > >> like here: http://archive.ambermd.org/201103/0431.html > >> > >> So I'll got back again on my research and adjust my "mind" on the actual > >> bleeding edge simulations > >> taking into account all the recent code and force fields progresses. > >> > >> Best, > >> > >> Stéphane > >> > >> -- > >> Team Protein Design In Silico > >> UFIP, UMR 6286 CNRS, > >> UFR Sciences et Techniques, > >> 2, rue de la Houssinière, Bât. 25, > >> 44322 Nantes cedex 03, France > >> Tél : +33 251 125 636 > >> Fax : +33 251 125 632 > >> http://www.ufip.univ-nantes.fr/ - http://www.steletch.org > >> > >> -- > >> Gromacs Users mailing list > >> > >> * Please search the archive at http://www.gromacs.org/ > >> Support/Mailing_Lists/GMX-Users_List before posting! > >> > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > >> * For (un)subscribe requests visit > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >> send a mail to gmx-users-requ...@gromacs.org. > >> > > > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Avg. Volume in NPT by Small Coupling Time
Hi, I think that's fine for rapidly forcing the volume to be close to the right equilibrium value, with low fluctuations. Then switch to gentler NPT (or constant-volume) for making a proper observation of the pressure. Mark On Thu, Nov 6, 2014 at 4:44 PM, Johnny Lu wrote: > Hi. > > How to get an accurate average volume for a system, such that the pressure > will be at 1 bar in a subsequent NVT run using this average volume? > > Is it ok to use Berendsen barostat with a very small time constant (0.2 ps) > ? > (At first I picked 0.1ps, gromacs 4.6.7 told me to use at least 0.2 ps). > > I was hoping that a smaller time constant would allow the simulation to > sample the volume more frequently and Berendsen barostat would help the > system to converge to the correct average volume faster. > > What are the possible draw backs? > > So far (2 ns), I see that the pressure fluctuation is smaller than a PR > barostat. > > It seems to be fine to use Berendsen barostat for this purpose ( [ > > https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2011-February/058453.html > ] > ) > > Thank you again. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] gmx covar (Version 5.x) segfaults with covariance matrices bigger than 1500x1500
On Thu, Nov 6, 2014 at 4:35 PM, Machtens, Jan-Philipp < j.macht...@fz-juelich.de> wrote: > Hi, > yes I will post that to redmine soon, but let me first clarify the issue, > since I tested some more conditions in the meantime. > (I realized that my trajectory had 1501 frames and the error occured when > I choose more than 500 atoms, i.e. when the number of degrees of freedom > becomes larger then the number of frames). > So in general, if your trajectory has nf frames, g_covar will result in a > segfault if the group to be (covariance) analyzed is larger then nf/3 atoms. > If found this statement to be true for gromacs 4.6.6, 4.6.7 and 5.0.2. > This error does not happen for gromacs 4.6.5 > > So, I wonder whether this is an unwanted behaviour which has been > introduced in 4.6.6? Do you think this behavior makes sense ? The official > release notes for 4.6.6 do not mention changes in g_covar. > Correct, but a change (git hash 972032bfb8) that was intended to fix a problem observed with g_anaeig also affected code in g_covar (which I have now corrected in the release notes). The nature of the change seems very consistent with your observations. Mark Best, > Jan-Philipp Machtens > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [ > gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Mark > Abraham [mark.j.abra...@gmail.com] > Sent: Thursday, November 06, 2014 1:27 PM > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] gmx covar (Version 5.x) segfaults with covariance > matrices bigger than 1500x1500 > > Hi, > > IIRC some minor bugs were fixed, but a regression like that should be dealt > with... please file at http://redmine.gromacs.org. > > Mark > > On Thu, Nov 6, 2014 at 12:00 PM, Machtens, Jan-Philipp < > j.macht...@fz-juelich.de> wrote: > > > Dear all, > > I observed that g_covar in Gromacs 5.0.2 segfaults at the diagonalization > > step, if the group for the covariance analysis is bigger than 500 atoms, > > i.e. if the covariance matrix is bigger than 1500x1500. > > In my hands, this problem does not arise with g_covar 4.6.x. The results > > obtained from g_covar (version 5.x) on groups <= 500 atoms that I > obtained > > were the same os those from version 4.6.x and also verified manually. > > Memory is not the problem here. The problem is independent on > single/double > > precision. > > > > Before posting this on redmine.gromacs I first want to check whether > > someone here has made a contradicting experience which would argue > against > > a possible bug introduced in 5.0.2? > > Thanks. > > Cheers, > > Jan-Philipp Machtens > > > > > > > > > > > > > > > > Forschungszentrum Juelich GmbH > > 52425 Juelich > > Sitz der Gesellschaft: Juelich > > Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 > > Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher > > Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), > > Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, > > Prof. Dr. Sebastian M. Schmidt > > > > > > > > > > > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/M
Re: [gmx-users] Discrepancy in a single point energy simulation between Gromacs and Namd.
Hi, Best practice for single-points is here http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy, but you are fortunately avoiding most of the issues by not using constraints. Last time someone reported a discrepancy like this (AMBER, IIRC) there was a difference in the way the two codes were shifting the non-bonded potential to be zero at the cutoff. Your .mdp forces Gromacs to use no shifts, but I don't know whether you have done so for NAMD, if it is needed and/or possible. You can try coulomb_modifier = potential-shift. Mark On Fri, Nov 7, 2014 at 5:45 PM, IÑIGO SAENZ wrote: > Hi all, > > I've got a system of a protein inside a cube of water parametrized with the > amber ff99SB force-field. I have converted the .prmtop and .pdb files of > this system into a .gro and .top by means of ACPYPE. The problem is that > when I perform the single point energy calculation of these system with > Namd and Gromacs I obtain very opposing results in the Electrostatic energy > results and I suspect that I'm overlooking some details in the .mdp file > or in the namd input file. I paste you the results that I obtain with NAMD > and gromacs and also the configuration files. > > > BOND: 38088.4829 38081.7399 > ANGLE:1573.6867 1573.7189 > DIHEDRAL: 9873.2782 9872.7127 > COULOMB: -179655.6187 141241 (1-4 interactions) -1.84836e+07 (short > range) > VDW: 21796.8418 21797.2514 > > First column corresponds to NAMD results and the second one to Gromacs > results, > Now, the *SPE.mdp file* > > define = -DFLEXIBLE > integrator = md > nsteps = 0 > dt = 0.001 > constraints = none > nstcomm = 1 > ns_type = simple > nstlist = 1 > coulombtype = cut-off > vdw_modifier = none > coulomb_modifier = none > rlist= 0.9 > rcoulomb = 0.9 > rvdw = 0.9 > Tcoupl = no > Pcoupl = no > gen_vel = no > nstxout = 1 > pbc = xyz > nstlog = 1 > nstenergy= 1 > nstvout = 1 > nstfout = 1 > nstxtcout= 1 > comm_mode= ANGULAR > continuation = yes > > *NAMD.conf file:* > > rigidBonds none > timestep 2 > temperature0 > cutoff 9 > switching off > PMEoff > cellBasisVector1 117.210 0 0 > cellBasisVector2 0 94.119 0 > cellBasisVector3 0 0 78.923 > # NAMD doesn't force neutralisation of charge > amber on # Specify this is AMBER force field > parmfile parameters # Input PARM file > ambercoor s.inpcrd # Input coordinate file > outputname run_namd # Prefix of output files > excludescaled1-4 > 1-4scaling 0.8333 # =1/1.2, default is 1.0 > run0 ;# 2ps > > I should mention that in .gro I put the box size correctly, the same values > that the box-size values that appear in the NAMD.conf file divided by 10 to > convert them to nanometers. > > I'm desperate with this error, please, any help would be highly > appreciated! If you need more information about this problem, feel free to > ask me. > > Thank you very much in advance! > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Dyn. Load Balance changes Cut off
Hi, This is normal. See http://www.gromacs.org/Documentation/Acceleration_and_parallelization#Hybrid.2fheterogeneous_acceleration and manual 3.17.5. The quality of the approximation to full electrostatics is the thing that should be conserved, not the cut-off. In the bad old days, the cut-off was the only parameter available, but this is not true with PME. Mark On Fri, Nov 7, 2014 at 7:21 PM, Johnny Lu wrote: > Hi. > > When I read the log file, I see: > > PP/PME load balancing changed the cut-off and PME settings: >particle-particlePME > rcoulomb rlistgrid spacing 1/beta >initial 1.000 nm 1.090 nm 64 64 64 0.117 nm 0.320 nm >final1.302 nm 1.392 nm 48 48 48 0.156 nm 0.417 nm > cost-ratio 2.08 0.42 > (note that these numbers concern only part of the total PP and PME load) > > So, the cut off that I typed in the mdp file was changed. > > Will that affect the result of the simulation? I'm using gromacs 4.6.7. > Or any cut off will be fine, as long as I use a cut off that is long > enough? > > The force field paper for Amber99SB-ILDN used 1.0 nm for both VdW and PME > electrostatic cut off. > > Thanks again. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] CMake Errors when installing gromacs-5.0.2 with Orca
Hi, You've somehow made the normal Gromacs source files missing or unreadable... start afresh? And use your normal account until you need to make install? Mark On Fri, Nov 7, 2014 at 8:47 PM, Matthew Kelley < matthewkelley2...@u.northwestern.edu> wrote: > Hello, > > I'm trying to install gromacs-5.0.2 on our local cluster with Orca using > CMake 3.0, and I'm running into a few issues. With a cmake command along > the lines of the following, > > cmake .. -DGMX_QMMM_PROGRAM=ORCA -DGMX_BUILD_OWN_FFTW=ON -DGMX_MPI=ON > -DCMAKE_INSTALL_PREFIX=/my_path/GROMACS-ORCA/ -DCMAKE_CXX_COMPILER=g++ > -DCMAKE_C_COMPILER=gcc > > I get errors in the terminal that look like > > > You have called ADD_LIBRARY for library testutils without any source files. > This typically indicates a problem with your CMakeLists.txt file > -- Check if the system is big endian > -- Searching 16 bit integer > -- Using unsigned short > -- Check if the system is big endian - little endian > -- Looking for inttypes.h > -- Looking for inttypes.h - found > CMake Error at src/gromacs/gmxlib/CMakeLists.txt:46 (list): > list sub-command REMOVE_ITEM requires two or more arguments. > > > CMake Error at src/gromacs/legacyheaders/CMakeLists.txt:41 (list): > list sub-command REMOVE_ITEM requires two or more arguments. > > > CMake Error at src/gromacs/legacyheaders/CMakeLists.txt:42 (list): > list sub-command REMOVE_ITEM requires two or more arguments. > > > -- Performing Test HAS_NO_UNUSED_PARAMETER > -- Performing Test HAS_NO_UNUSED_PARAMETER - Success > -- Performing Test HAS_NO_DEPRECATED_REGISTER > -- Performing Test HAS_NO_DEPRECATED_REGISTER - Success > You have called ADD_LIBRARY for library mdrun_objlib without any source > files. This typically indicates a problem with your CMakeLists.txt file > You have called ADD_LIBRARY for library view_objlib without any source > files. This typically indicates a problem with your CMakeLists.txt file > -- Configuring incomplete, errors occurred! > > -- > > I'm not sure what I should be looking for in the log files or if I need to > fix my CMakeLists.txt file. I am running the cmake command from the > directory "build" inside the root gromacs-5.0.2 source directory. Please > let me know what I should do to correct these errors. I can add requisite > information from the log files if required. > > Thank you, > Matthew > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] dynamic cross-correlation maps and older gromacs binaries
On Sat, Nov 8, 2014 at 12:19 PM, Rethi Madathil wrote: > Dear All, > > I am interested in generating dynamic cross-correlation maps to show the > correlated and anti-correlated motion of bound and unbound protein. > > (for the reference see (e.g > > http://www.pnas.org/content/suppl/2013/06/18/1309755110.DCSupplemental/sapp.pdf > Fig S10). See the image below > > However g_correlation will work with only gromacs-3.3 as the developers > have confirmed it. The develops suggested to older gromacs version as > g_correlation can still take gromacs4.5 .xtc files. I tried to download the > old gromacs binaries but there seems to be problem. > > I would appreciate if someone can shed some light on > > 1) if older binaries are available and where to download them > If Google doesn't know, nobody does! Get the source and build it. IIRC 3.3 had build instructions in the tarball. Mark 2) if there any other alternative ( I know modified g_covar by Ran Friedman > is there but that is also an old program and will not work newer gromacs > version) > > > 3) can we generate cross-correlation map by using g_covar by providing the > option -ascii and using the dat file generated to plot these maps in > matlab. Does anyone have some matlab scripts to do that. > > If anyone know better method, tips, comments/suggestion that would be > highly appreciated. > > Regards, > > Madathil > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] nvt problem
Hi,
You've got too many sources of possible complications. Simplify. Does gold
in water work? With and without freeze groups? Does peptide in water work?
Why aren't you generating velocities at the right temperature for the start
of your NVT?
Mark
On Sat, Nov 8, 2014 at 6:10 AM, Lovika Moudgil
wrote:
> Hi Everyone ,
>
> I am having a problem in NVT of system . In my system I have Gold and
> aminoacid . For Gold I am using GolP forcefield and for aminoacid using
> OPLSAA forcefield . I have done energy minimization of my system but when I
> am doing NVT I am getting error of water is not getting settled . I am
> confused How it got minimize if water is not settled in system .I have
> tried changing parameters of NVT.mdp file but noting worked . Can any body
> help me what can be the root cause for this . I will be thankful for
> guidance .
>
> My NVT.mdp
> ; 7.3.2 Preprocessing
> define = -DPOSRES ; defines to pass to the
> preprocessor
>
> ; 7.3.3 Run Control
> integrator = md; md integrator
> tinit = 0 ; [ps] starting time for
> run
> dt = 0.001 ; [ps] time step for
> integration
> nsteps = 25000 ; maximum number of steps
> to integrate, 0.001 * 25,000 = 25 ps
> nstcomm = 1 ; [steps] frequency of mass
> motion removal
> comm_grps = Protein Non-Protein ; group(s) for center of
> mass motion removal
>
> ; 7.3.8 Output Control
> nstxout = 25000 ; [steps] freq to write coordinates
> to trajectory
> nstvout = 25000 ; [steps] freq to write velocities
> to trajectory
> nstfout = 25000 ; [steps] freq to write forces to
> trajectory
> nstlog = 50 ; [steps] freq to write energies to
> log file
> nstenergy = 100 ; [steps] freq to write energies to
> energy file
> nstxtcout = 100 ; [steps] freq to write coordinates
> to xtc trajectory
> xtc_precision = 1000 ; [real] precision to write xtc
> trajectory
> xtc_grps= System; group(s) to write to xtc
> trajectory
> energygrps = System; group(s) to write to energy file
>
> ; 7.3.9 Neighbor Searching
> nstlist = 1 ; [steps] freq to update neighbor
> list
> ns_type = grid ; method of updating neighbor list
> pbc = xyz ; periodic boundary conditions in
> all directions
> rlist = 1.4 ; [nm] cut-off distance for the
> short-range neighbor list
>
> ; 7.3.10 Electrostatics
> coulombtype = PME ; Particle-Mesh Ewald
> electrostatics
> rcoulomb= 1.4 ; [nm] distance for Coulomb cut-off
>
> ; 7.3.11 VdW
> vdwtype = cut-off ; twin-range cut-off with rlist
> where rvdw >= rlist
> rvdw= 1.4 ; [nm] distance for LJ cut-off
> DispCorr= EnerPres ; apply long range dispersion
> corrections
>
> ; 7.3.13 Ewald
> fourierspacing = 0.10 ; [nm] grid spacing for FFT grid
> when using PME
> pme_order = 4 ; interpolation order for PME, 4 =
> cubic
> ewald_rtol = 1e-5 ; relative strength of
> Ewald-shifted potential at rcoulomb
>
> ; 7.3.14 Temperature Coupling
> tcoupl = nose-hoover ; temperature
> coupling with Berendsen-thermostat
> tc_grps = ProteinNon-Protein; groups to couple
> seperately to temperature bath
> tau_t = 0.10.1; [ps] time
> constant for coupling
> ref_t = 310310; [K] reference
> temperature for coupling
>
> ; 7.3.17 Velocity Generation
> gen_vel = no ; generate velocities according to
> Maxwell distribution of temperature
> gen_temp= 310 ; [K] temperature for Maxwell
> distribution
> gen_seed= -1; [integer] used to initialize
> random generator for random velocities
>
> ; 7.3.18 Bonds
> constraints = all-bonds ; convert all bonds to constraints
> constraint_algorithm= LINCS ; LINear Constraint Solver
> lincs_order = 4 ; highest order in the expansion of
> the contraint coupling matrix
> lincs_iter = 1 ; number of iterations to correct
> for rotational lengthening
> lincs_warnangle = 80; [degrees] maximum angle that a
> bond can rotate before LINCS will complain
> ; To keep au surface in place, freeze Au atoms.
> ; The AU group has been defined via make_ndx
> ; to contains all the AU atoms ('a AU').
> freezegrps = AU AUI
> freezedim
Re: [gmx-users] Installing GROMACS 4.6.7 on Intel Cluster
Hi, This means that "make" is somehow running out of memory. That should never happen, but what's going wrong for you is impossible for us to tell. Switching compiler won't help - the compiler is not used in the installation phase. Mark On Sun, Nov 9, 2014 at 1:42 AM, Agnivo Gosai wrote: > Dear Users > > I figured out from the trailing mails as to how to use the "new installed > version of CMAKE" for installing GROMACS > > I used -DGMX_BUILD_OWN_FFTW=ON -DCMAKE_INSTALL_PREFIX=. . > By default I think "icc" and "icpc" compilers were chosen. > > This step progressed smoothly. So , next I issued the command : "make". > This step also completed without any error messages. > > However "make install" did not finish as expected. The installation process > looked like a never ending process. Ultimately the following error message > came up : > > terminate called after throwing an instance of 'std::bad_alloc' > what(): std::bad_alloc > make: *** [install] Aborted > > I do not understand what to do next. I am thinking of using "gcc" and "g++" > now. Kindly provide further suggestions. > > > > > > -- Forwarded message -- > From: Mohd Farid Ismail > To: "gmx-us...@gromacs.org" , " > gromacs.org_gmx-users@maillist.sys.kth.se" < > gromacs.org_gmx-users@maillist.sys.kth.se> > Cc: > Date: Sat, 08 Nov 2014 09:19:14 +0800 > Subject: Re: [gmx-users] Installing GROMACS 4.6.7 on Intel Cluster > What he meant was to specify full path of your cmake, i.e. > /work/user/GROMACS/cmake-2.8/bin/cmake .. -DGMX_FFT_LIBRARY. (and so > on); instead of just typing cmake .. -DGMX_FFT_LIBRARY > > This is really a linux issue instead of gromacs. > > > 08.11.2014, 06:00, "Agnivo Gosai" : > > Dear Users > > 1 . I am not sure as to how to set the full path in the cmake command line. > Do I need to use the export command to set the path ? > > An example will be of great help. I am also searching the web but can not > find a satisfactory answer. > > As highlighted in my step 5 ( trailing mail ) , I think install_prefix will > install the gromacs version in the specified directory or am I wrong ? > > 2. Yes , I understand it after reading the instructions. I think mdrun will > pick up MPI threading automatically. > > I have also installed FFTW 3.0 in a local folder , how do I set its path in > the cmake command line and I also have gcc in the root folder , along with > icc. > > Pardon my ignorance as I think these are very basic questions related to > the linux architecture. > > -- Forwarded message -- > From: Justin Lemkul > To: gmx-us...@gromacs.org > Cc: > Date: Fri, 07 Nov 2014 16:26:56 -0500 > Subject: Re: [gmx-users] Installing GROMACS 4.6.7 on Intel Cluster > > > On 11/7/14 4:20 PM, Agnivo Gosai wrote: > Dear Users > > I checked and found that the CMAKE version installed in my university > cluster is 2.6-patch 4 however GROMACS 4.6.7 requires CMAKE 2.8 or higher. > So I installed CMAKE 2.8.11 in my local work directory : > /work/user/GROMACS/cmake-2.8/ > > bin/cmake > > Now I want to use Intel MKL , so after reading the GROMACS installation > instruction I have decided to use the following workflow :- > > 1. tar xfz gromacs-4.6.7.tar.gz > 2. cd gromacs-4.6.7 > 3. mkdir build > 4. cd build > 5. cmake .. -DGMX_FFT_LIBRARY=mkl -DGMX_MPI=ON - > DCMAKE_INSTALL_PREFIX=/work/user/GROMACS > 6. make > 7. make install > Now when I check install location of CMAKE it points to the old version > located in the Cluster root directory. > > Now , I want to use the new version which I believe to have installed > correctly. So please help in solving this problem. > > Specify the full PATH of your cmake, otherwise the environment will just > pick up the default cmake on the cluster. > > Also I would request the users to check my workflow of the installation > > process and provide suggestions. > > There is no point in compiling the whole suite of tools with MPI; nothing > makes use of MPI except mdrun. So if you want to compile all the tools > (preprocessing and analysis), don't set GMX_MPI. If you are using GMX_MPI, > then set -DGMX_BUILD_MDRUN_ONLY=ON to get MPI-enabled mdrun. Strictly > speaking, MPI is not required, but it depends on what you want to do > whether or not you need it. > > -Justin > > - > Thanks & Regards > Agnivo Gosai > Grad Student, Iowa State University. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at ht
Re: [gmx-users] Installing GROMACS 4.6.7 on Intel Cluster
Hi, Set CMAKE_INSTALL_PREFIX to where you want Gromacs to be installed so that you know where it is and can find it. Do not choose the same directory as the tarball unpacks to! I suspect this is leading to some infinite loop while trying to install new copies of files that you just installed because you just installed new copies of the files you just installed... Mark On Mon, Nov 10, 2014 at 1:12 AM, Agnivo Gosai wrote: > Dr. Szilard : > > Yes , firstly I move inside the unzipped gromacs-4.6.5 folder then I create > a build directory , then I run the cmake .. commands in the terminal. I > follow the installation guide. > > As cmake 2.6.4 is installed in the root of the cluster and I need cmake 2.8 > , so I installed it in this directory :- > > /work/gb_lab/agosai/GROMACS/cmake-2.8.11/bin > > And this is the path to the gromacs-4.6.5 build directory : > > /work/gb_lab/agosai/GROMACS/gromacs-4.6.5/build > > This is my last installation command : > > /work/gb_lab/agosai/GROMACS/cmake-2.8.11/bin/cmake .. > -DGMX_BUILD_OWN_FFTW=ON > -DCMAKE_INSTALL_PREFIX=/work/gb_lab/agosai/GROMACS/gromacs-4.6.5 > -DCMAKE_C_COMPILER=icc -DCMAKE_CXX_COMPILER=icpc > > What do you mean by source tree ? I beg your pardon for my ignorance but I > confess that I am a newcomer in the Linux world. > > > - Forwarded message -- > From: "Szilárd Páll" > To: Discussion list for GROMACS users > Cc: Discussion list for GROMACS users < > gromacs.org_gmx-users@maillist.sys.kth.se> > Date: Mon, 10 Nov 2014 00:52:44 +0100 > Subject: > > There is something *very* weird happening here, it looks like cmake > ends up in some kind of recursion and just before it crashes it is > installing in a directory which contains '/gromacs' about 300 times. > > My first guess is that you are installing in the same directory where > your build (and source tree?) is. Is that the case? > > -- > Szilárd > > > On Mon, Nov 10, 2014 at 12:31 AM, Agnivo Gosai > wrote: > > Dear Users > > > > Dr.Szilard : I searched in the web regarding the correct syntax and as > you > > wrote in the last mail , ran it again. > > > > The generated log file is huge. 260 MB. So I am sending a Google Drive > > link. If possible kindly check and suggest further. > > > Thanks & Regards > Agnivo Gosai > Grad Student, Iowa State University. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] New problem GROMACS 4.6.7 in Intel Cluster
On Mon, Nov 10, 2014 at 2:17 AM, Justin Lemkul wrote: > > > On 11/9/14 8:15 PM, Agnivo Gosai wrote: > >> Dear Users >> >> Firstly thanks (specially Drs. Szilard and Mark ) for helping me out with >> the installation of GROMACS 4.6.7 on my university Intel cluster. However >> I >> ran into a new problem while using it. >> >> 1. Firstly I used pdb2gmx to process a pdb file. >> 2. Then I used editconf. >> 3. Then I used genbox. >> >> But I encountered with the following error. >> >> Initialising van der waals distances... >> Will generate new solvent configuration of 5x5x9 boxes >> Generating configuration >> Sorting configuration >> Found 1 molecule type: >> SOL ( 3 atoms): 48600 residues >> Calculating Overlap... >> box_margin = 0.315 >> Removed 53454 atoms that were outside the box >> OMP: Error #178: Function pthread_getattr_np failed: >> OMP: System error #12: Cannot allocate memory >> Aborted >> >> Now upon searching on the web it seems to be an OpenMP error. Again I am >> in >> a fix which I have little or no idea about. >> >> > Preprocessing tools (and most analysis tools) are not parallelized in any > way. They run on one core only. Generally you do not carry out these sorts > of operations on a cluster, as there is no benefit to doing so. > True, and the particular problem is likely that Agnivo has not prepared the environment correctly, e.g. by sourcing Intel's compilervars.sh script, and/or following the cluster's usage guide for loading its Intel module. Mark > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > == > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Ligand is not in the same position as in PDB file
Hi, Probably you are seeing normal behaviour in the presence of http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions. If you want to visualize the protein and ligand as a complex, you need to post-process the output accordingly. mdrun doesn't know that you plan to treat them as special. Mark On Tue, Nov 11, 2014 at 9:50 AM, neha bharti wrote: > Hello All > > I am trying to perform MD for protein-ligand complex in popc lipid with > charmm36 force field and also follow Justin A. Lemkul tutorial. > I downloaded the pdb structure of protein and ligand complex and the > separate the protein and ligand file and prepare the system. > > Finally I perform the MD run for 100 ns, I found that the ligand is not in > the same place as present in PDB file of protein ligand complex. > > Is it necessary that the protein should be in the same position as present > in protein ligand complex PDB file ?? > > Is there something wrong in my work. > > Please Help. > > Thanks and regards > > Neha Bharty > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] energy minimization of protein taken from PDB
Hi, That value may indicate that the ligand is not horribly out of place, because the total energy is negative. Showing a favourable binding interaction is a different matter, for which this is just the tiniest first step. Mark On Tue, Nov 11, 2014 at 9:04 AM, md kashif wrote: > Dear Dr. Justin Lemkul > Thanks for your kind suggestion, I have energy minimized my protein taken > from PDB. It gives result as -1.5248922e+06. Taking the energy minimized > protein generated in .gro file file and docking it with ligand and doining > energy minimization again, it gives result as -1.0504211e+06. > Is this value correct? Is my ligand showing interaction and bound to my > protein. Please help. > > > Thanking You > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Ligand is not in the same position as in PDB file
Hi, Did you consult the link I provided? ;-) Mark On Tue, Nov 11, 2014 at 11:18 AM, neha bharti wrote: > Thank you very much mark for your reply. > I merge the protein and ligand file before starting the molecular dynamics > simulation. > Then I start the MD run. > I don't how to post-process the output. can you please tell me how to > perform it or is there any article or tutorial available for that. > > Thanks and regards > Neha Bharty > > > >Hi, > > >Probably you are seeing normal behaviour in the presence of > > > http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions > < > http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions > > > . > >If you want to visualize the protein and ligand as a complex, you need to > >post-process the output accordingly. mdrun doesn't know that you plan to > >treat them as special. > > >Mark > > >On Tue, Nov 11, 2014 at 9:50 AM, neha bharti > >wrote: > > >> Hello All > >> > >> I am trying to perform MD for protein-ligand complex in popc lipid with > >> charmm36 force field and also follow Justin A. Lemkul tutorial. > >> I downloaded the pdb structure of protein and ligand complex and the > >> separate the protein and ligand file and prepare the system. > >> > >> Finally I perform the MD run for 100 ns, I found that the ligand is not > in > >> the same place as present in PDB file of protein ligand complex. > >> > >> Is it necessary that the protein should be in the same position as > present > >> in protein ligand complex PDB file ?? > >> > >> Is there something wrong in my work. > >> > >> Please Help. > >> > >>Thanks and regard > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] GROMACS 5 - problem with LINCS with freeze groups
Hi, You are using settings that trigger the group-scheme twin-range code. There's been a code bug there for a very long time, which we fixed after 4.6.5 (see http://redmine.gromacs.org/issues/1400. "Normal" usage such as in your .mdp file also tended to be broken when simulating water, which masked the code bug; your 4.6.5 run may look smooth, but probably the thermostat is hiding the systematic problem of nstlist*dt being too large to properly model water libration, and the symptoms of the virial problem we fixed are lost in the noise. If you can try 4.6.7, I expect that you will observe the same problems you see in 5.0.x. That will help us know what to consider fixing. We certainly didn't test the freeze-group functionality, so we could well have introduced a new problem, such as adding force components that were already zeroed for freezing. If I'm right about 4.6.7 also being broken, please file an issue at http://redmine.gromacs.org with a tarball of your grompp input files. Mark On Tue, Nov 11, 2014 at 2:05 PM, Tomek Wlodarski wrote: > Hi, > > I experience some strange behaviour and I wonder if this is a bug or I am > doing something wrong. > I am running test simulation to check freeze groups in new gromacs. > And I am getting LINCS Warnings for atoms which should be frozen...: > > Step 0, time 0 (ps) LINCS WARNING > relative constraint deviation after LINCS: > rms nan, max inf (between atoms 30 and 31) > bonds that rotated more than 30 degrees: > atom 1 atom 2 angle previous, current, constraint length > 32 33 90.80.1010 23.4699 0.1010 > 32 34 90.30.1010 71.2488 0.1010 > [...] > > my mdp file: > > ; RUN CONTROL PARAMETERS > integrator = md > dt = 0.002 ; 2 femtosecond time step for > integration > nsteps = 50 ; 1ns > > ; OUTPUT CONTROL OPTIONS > nstxout = 5000; save coordinates every 2 ps > nstvout = 5000; save velocities every 2 ps > nstenergy = 5000; save energies every 2 ps > nstlog = 5000; update log file every 2 ps > energygrps = Protein Non-Protein > nstxtcout= 5000 > xtc-grps = non-Water > > ; NEIGHBORSEARCHING PARAMETERS > nstlist = 5 > ns-type = Grid > cutoff-scheme= group > pbc = xyz > rlist= 0.9 > > ; OPTIONS FOR ELECTROSTATICS AND VDW > coulombtype = pme > rcoulomb = 0.9 > fourierspacing = 0.12 > ewald_rtol = 1e-5 > fourier_nx = 0 > fourier_ny = 0 > fourier_nz = 0 > optimize_fft = yes > vdw-type = Cut-off > rvdw = 1.2 > energygrp_table = > > ; Temperature coupling > Tcoupl = V-rescale > tc-grps = ProteinNon-Protein > tau_t= 0.10.1 > ref_t= 300300 > > ; Freeze atoms > freezegrps = Protein > freezedim= Y Y Y > energygrp-excl = Protein Protein > > ; Pressure coupling > pcoupl = no > > ;Velocity generation > gen_vel = no > gen_temp = 300 > gen_seed = -1 > > ;Constrain all bonds > constraints = all-bonds > constraint-algorithm = Lincs > lincs_iter = 2 ; accuracy of LINCS > lincs_order = 6; also related to accuracy > > Exactly the same system with the same mdp file I am running in Gromacs > 4.6.5 and everything runs smoothly. > Any suggestions? > Thanks a lot! > Best > > tomek > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] restarting of shifted potential, 4.6.7 bug?
On Tue, Nov 11, 2014 at 3:38 PM, Johnny Lu wrote: > Hi. > > I ran 30ns NPT with Potential-shift-Verlet on both potentials, continuing > from a NPT without Potential-shift-Verlet. The energy dropped from -3e5 to > -4e5, which is fine. > > After that, I continue the 30ns NPT with the same mdp file, except with a > longer run time (300ns). > > The total energy was -4e5 at step 0, and then -3e5 at step 5000, and now at > about 25 ns, it goes back to -3.5e5. Why the energy suddenly changed after > step 0? > IIRC, the restart ought to compute the same energy on the initial coordinates as it did at the end of the previous run, and even if there's no re-computation on the same coordinates, obviously it should not jump by 1e5 in a few steps (or one? can't tell from the resolution). I would think that might be a bug in filling a data structure for the output, but probably not one in the simulation itself. Please file an issue at http://redmine.gromacs.org, tarballing all the relevant files, and I'll try to look at it. The long-time behaviour of both simulations is pretty suspect though. Since you're prepared to be ultra-conservative with your non-bonded and SETTLE settings, I would explore using a 0.5fs time step (in normal and ultra-conservative mode). Berendsen is not a good barostat algorithm for production work, too... but I would not expect such a problem from its use. Perhaps more importantly, why are you turning off the long-range dispersion correction? Mark I used the same machine and same mixed precision gromacs 4.6.7 mdrun and > grompp for both simulations. > > The plot of total energies for the two simulations: > http://oi60.tinypic.com/ddmejd.jpg > The two mdp files: http://oi58.tinypic.com/11980si.jpg > > The commands that I used for continuing the simulations: > > The previous simulation (npt14): ../../sofware/gromacs-4.6.7/bin/grompp -f > npt14.mdp -c npt13.tpr -t npt13_step22620750.cpt -o npt14.tpr > > The current simulation (npt15): ../../sofware/gromacs-4.6.7/bin/grompp -f > npt15.mdp -c npt14.tpr -t npt14_step3000.cpt -o npt15.tpr > > Thanks. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] adding an acid as n-terminus
On Thu, Nov 13, 2014 at 11:45 AM, Velia Minicozzi < velia.minico...@roma2.infn.it> wrote: > Dear gmx-users, > > we want to simulate a peptide which starts with an acidic terminus. > We used PRODRG to compute the coordinates and the FF for this new > residue and we followed all the gromacs instructions to insert a new > residue (http://www.gromacs.org/Documentation/How-tos/Adding_ > a_Residue_to_a_Force_Field) > > Following the instructions, we inserted the new residue in the > gromos43a1ff rtp file and > we changed the hdb file accordingly. > Pdb2gmx give us the following error that we do not understand. > > What else should we change? > You want to get pdb2gmx to build your polypeptide, so the topology you got from PRODRG must be modified so that it follows the .rtp format, and has the right + or - indicators to show where the bonds to other residues will form. You haven't showed your work there, so we're left guessing unproductively. > We add to the email the pdbfile and the itp file computed by PRODRG > > pdb2gmx -f provapept2.pdb -o provapept2.gro -p topol2.top -ignh -ter > . > > Fatal error: > Residue 2 named ACI of a molecule in the input file was mapped > to an entry in the topology database, but the atom C used in > that entry is not found in the input file. Perhaps your atom > and/or residue naming needs to be fixed. This means what it says. pdb2gmx recognized in your .pdb file an ACl residue that it found in your .rtp database, but the .pdb file had no atom named C. Whether it should depends on things you haven't told us. Mark > > -- > > Velia Minicozzi > > Universita' di Roma Tor Vergata > Dipartimento di Fisica > via della Ricerca Scientifica 1, I-00133 ROMA, Italy > Tel. +39.06.7259.4440Fax +39.06.2023.507 > Email: minico...@roma2.infn.it > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Doubt about g_energy.
Hi, No. These numbers have been stored in single precision, so there are only ~6 significant digits. A form of scientific notation is clearly preferable to printing 7553440. Mark On Thu, Nov 13, 2014 at 11:46 AM, IÑIGO SAENZ < inigo.saen...@estudiant.upf.edu> wrote: > Hi, > > I'm running g_energy to check single points' energies and I'm getting the > following results. > > Energy Average Err.Est. RMSD Tot-Drift > > --- > Bond57100.1 -- 0 0 > (kJ/mol) > Angle 22261.2 -- 0 0 > (kJ/mol) > Proper Dih. 1407.47 -- 0 0 > (kJ/mol) > Ryckaert-Bell. 7155.24 -- 0 0 > (kJ/mol) > LJ-14 12079.9 -- 0 0 > (kJ/mol) > Coulomb-14 17097.3 -- 0 0 > (kJ/mol) > LJ (SR) 7.55344e+06 -- 0 0 > (kJ/mol) > Coulomb (SR) -34118.9 -- 0 0 > (kJ/mol) > > Is there any way of avoiding the use of "e" notation when showing big > numbers? I would like to get the LJ (SR) in a normal decimal way, as the > other energies. > > Thank you very much! > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Extra number of bonds created than specified (ZN-CYS)
Hi, You seem to be suggesting that there is an entry in [bonds] that is 4800 to 3368, and three others from that cysteine residue. That's highly surprising, because this kind of workflow seems like something people should have tried before... If so, then it would be good to file a report at http://redmine.gromacs.org with your Gromacs version, input files and pdb2gmx call, so that we can reproduce it and fix it. You can of course delete the lines with the spurious [bonds] entry. grompp might complain if there are [angles] or [dihedrals] related to those, which you could also delete. You should verify that the final bonds+angles+dihedrals in the topology are what you think they should be. Mark On Fri, Nov 14, 2014 at 8:03 AM, Nixon Raj wrote: > Im dealing a protein with 4799 atoms and 1 ZN ion totally 4800 atoms. > > I need to form bonds between 4CYS-ZN , where i have equilibrium bond > length, force constant and partial charges for the same fixed. > > Since i have new partial charge for Zn ion , i have created an ZN ion in > name ZN1 . > > My specbond.dat is modified accordingly to add the necessary bonds , > > CYZ SG 1 ZN1 ZN 1 0.23CYZ ZN1 > > Running the pdb2gmx yielded me > > Linking CYZ-210 SG-3368 and ZN1-299 ZN1-4800... > > Linking CYZ-260 SG-4195 and ZN1-299 ZN1-4800... > > Linking CYZ-263 SG-4250 and ZN1-299 ZN1-4800... > > Linking CYZ-270 SG-4358 and ZN1-299 ZN1-4800... > > Start terminus MET-1: NH3+ > > End terminus TYR-298: COO- > > Opening force field file ./charmm36.ff/merged.arn > > Checking for duplicate atoms > > Generating any missing hydrogen atoms and/or adding termini. > > Now there are 299 residues with 4800 atoms > > Making bonds... > > Number of bonds was 4859, now 4859 > > Generating angles, dihedrals and pairs... > > Before cleaning: 12729 pairs > > Before cleaning: 12834 dihedrals > > Keeping all generated dihedrals > > Making cmap torsions...There are 296 cmap torsion pairs > > There are 12834 dihedrals, 838 impropers, 8752 angles > > 12621 pairs, 4859 bonds and 0 virtual sites > > Total mass 34700.069 a.m.u. > > Total charge -8.000 e > > Writing topology > > But i could find 12 extra bonds created with ZN1(4800) in my topology file. > But the dihedrals and angles are in correct numbers. > > Each residue sharing 4 bonds with ZN1 (4800), i.e) CA-ZN1, HB1-ZN1, HB2-ZN1 > and SG-ZN1 , where i need only one bond i.e) SG-ZN1 with each cystein > residue. > > Please help me to cross this roadblock. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Extra number of bonds created than specified (ZN-CYS)
On Fri, Nov 14, 2014 at 9:58 AM, Nixon Raj wrote: > Hi Mark > > Yeah i deleted it manually from the topology file and could able to > progress further. But how could this happen. > You really don't want to know ;-) > So its better to file a report as you suggested. Thanks > Please do. That code is nearly impossible to reason about, so the actual problem case is likely to be critical for fixing it. Mark > On Fri, Nov 14, 2014 at 4:50 PM, Mark Abraham > wrote: > > > Hi, > > > > You seem to be suggesting that there is an entry in [bonds] that is 4800 > to > > 3368, and three others from that cysteine residue. That's highly > > surprising, because this kind of workflow seems like something people > > should have tried before... If so, then it would be good to file a report > > at http://redmine.gromacs.org with your Gromacs version, input files and > > pdb2gmx call, so that we can reproduce it and fix it. > > > > You can of course delete the lines with the spurious [bonds] entry. > grompp > > might complain if there are [angles] or [dihedrals] related to those, > which > > you could also delete. You should verify that the final > > bonds+angles+dihedrals in the topology are what you think they should be. > > > > Mark > > > > On Fri, Nov 14, 2014 at 8:03 AM, Nixon Raj wrote: > > > > > Im dealing a protein with 4799 atoms and 1 ZN ion totally 4800 atoms. > > > > > > I need to form bonds between 4CYS-ZN , where i have equilibrium bond > > > length, force constant and partial charges for the same fixed. > > > > > > Since i have new partial charge for Zn ion , i have created an ZN ion > in > > > name ZN1 . > > > > > > My specbond.dat is modified accordingly to add the necessary bonds , > > > > > > CYZ SG 1 ZN1 ZN 1 0.23CYZ ZN1 > > > > > > Running the pdb2gmx yielded me > > > > > > Linking CYZ-210 SG-3368 and ZN1-299 ZN1-4800... > > > > > > Linking CYZ-260 SG-4195 and ZN1-299 ZN1-4800... > > > > > > Linking CYZ-263 SG-4250 and ZN1-299 ZN1-4800... > > > > > > Linking CYZ-270 SG-4358 and ZN1-299 ZN1-4800... > > > > > > Start terminus MET-1: NH3+ > > > > > > End terminus TYR-298: COO- > > > > > > Opening force field file ./charmm36.ff/merged.arn > > > > > > Checking for duplicate atoms > > > > > > Generating any missing hydrogen atoms and/or adding termini. > > > > > > Now there are 299 residues with 4800 atoms > > > > > > Making bonds... > > > > > > Number of bonds was 4859, now 4859 > > > > > > Generating angles, dihedrals and pairs... > > > > > > Before cleaning: 12729 pairs > > > > > > Before cleaning: 12834 dihedrals > > > > > > Keeping all generated dihedrals > > > > > > Making cmap torsions...There are 296 cmap torsion pairs > > > > > > There are 12834 dihedrals, 838 impropers, 8752 angles > > > > > > 12621 pairs, 4859 bonds and 0 virtual sites > > > > > > Total mass 34700.069 a.m.u. > > > > > > Total charge -8.000 e > > > > > > Writing topology > > > > > > But i could find 12 extra bonds created with ZN1(4800) in my topology > > file. > > > But the dihedrals and angles are in correct numbers. > > > > > > Each residue sharing 4 bonds with ZN1 (4800), i.e) CA-ZN1, HB1-ZN1, > > HB2-ZN1 > > > and SG-ZN1 , where i need only one bond i.e) SG-ZN1 with each cystein > > > residue. > > > > > > Please help me to cross this roadblock. > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > posting! > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > * For (un)subscribe requests visit > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > > send a mail to gmx-users-requ...@gromacs.org. > > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] How to add a repulsive harmonic potential
Hi, You can use a distance restraint (see manual) implemented with [bonds] type 10. In current released code, the atoms need to be within the same [moleculetype], which would likely mean you need to aggregate the ligands' topology definitions so that you can refer to atoms in different actual molecules that are now within the same [moleculetype] Alternatively, there is draft code for inter-molecular bonded interactions at https://gerrit.gromacs.org/#/c/2566/, but nobody has yet tried that it works. Mark On Fri, Nov 14, 2014 at 10:45 AM, wrote: > Dear all > > To avoid ligand aggregation under higher concentration, I would like to > introduce a weak repulsive potential term between the specific(e.g > nitrogen) atoms of ligand molecules in the Protein/Ligand/Water system. > This potential set as below. > U(R) = K(R-R0)^2, if R U(R) = 0, if R>R0 > > Could you tell me how to add the repulsive harmonic potential in MD > simulation? > > Bests, > Atsutoshi Okabe > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] IMPORTANT
Hi, Please use a descriptive subject. Your email is important to you, but that doesn't help anybody choose whether they might be able to help. :-) On Fri, Nov 14, 2014 at 12:30 PM, Anik Sen wrote: > Hei, > I am using gromacs 4.5 version, Since you are doing new work, you should very likely be using a more recent version of Gromacs, to get faster performance and generally fewer bugs. > and i wanted to incorporate a file in the residue. its just a small > molecule, h2o2. > I had to change the four files in the amber03 forcefield which i was using. > atomtypes.atp, ffbonded.itp, ffnonbonded.itp and incorporate a file at the > .rtp. > > Now atomtypes and .rtp file was done with no problem. > For ffnonbonded, i had the sigma and epsilon and so it was done. > For ffbonded.itp; > in the bond types there is are two terms b0 and kb, which i have changed. > in the angle types thers is the theta as th0 and another term 'cth'. What > is this 'cth' and its unit. > For dihedral types what are kd and pn and there units? > See the appropriate tables in manual sections in chapter 5 and links therefrom; more recent Gromacs versions have better documentation here, too. Mark I want to know what these terms represent not the value. > > Thanking you > Anik > > > > > > *** STK-14 Uppsala *** https://sites.google.com/site/stkmuu14/ > Dr. Anik Sen, > Post Doctoral Fellow, > Ångströmlaboratoriet- Uppsala Universitet > Box 538 > SE-751 21 Uppsala > Sweden > Phone no:- +46-722781705 > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] What is cth stand for, in the parameters file. It is not written in the latest manual 4.5.6.
On Fri, Nov 14, 2014 at 2:16 PM, Anik Sen wrote: > What is cth stand for, in the parameters file. It is not written in the > latest manual 4.5.6. The angle function *is* documented, in table 5.5, like I said. The notation is inconsistent between that table and the file you are using, but cth is the force constant. > Is kd the force constant for dihedral angles?? > Yes. See table 5.5 for units. Mark > > > [ bondtypes ] > ; ijfunc b0 > kb > C O 1 0.12300502080. > COM1 0.12500418400. > > > .. > [ angletypes ] > ; i jkfunc > th0cth > HOOAC1 > 109.500397.480 > HOOA CH1 1109.500 >397.480 > .. > > [ dihedraltypes ] > ;i j k l func > phase kd pn > CA CA CA OH 4 > 180.004.60240 2 > > with regards > Anik > > > Dr. Anik Sen, > Post Doctoral Fellow, > Ångströmlaboratoriet- Uppsala Universitet > Box 538 > SE-751 21 Uppsala > Sweden > Phone no:- +46-722781705 > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [ > gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Mark > Abraham [mark.j.abra...@gmail.com] > Sent: 14 November 2014 12:44:02 > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] IMPORTANT > > Hi, > > Please use a descriptive subject. Your email is important to you, but that > doesn't help anybody choose whether they might be able to help. :-) > > On Fri, Nov 14, 2014 at 12:30 PM, Anik Sen wrote: > > > Hei, > > I am using gromacs 4.5 version, > > > Since you are doing new work, you should very likely be using a more recent > version of Gromacs, to get faster performance and generally fewer bugs. > > > > and i wanted to incorporate a file in the residue. its just a small > > molecule, h2o2. > > I had to change the four files in the amber03 forcefield which i was > using. > > atomtypes.atp, ffbonded.itp, ffnonbonded.itp and incorporate a file at > the > > .rtp. > > > > Now atomtypes and .rtp file was done with no problem. > > For ffnonbonded, i had the sigma and epsilon and so it was done. > > For ffbonded.itp; > > in the bond types there is are two terms b0 and kb, which i have changed. > > in the angle types thers is the theta as th0 and another term 'cth'. What > > is this 'cth' and its unit. > > For dihedral types what are kd and pn and there units? > > > > See the appropriate tables in manual sections in chapter 5 and links > therefrom; more recent Gromacs versions have better documentation here, > too. > > Mark > > I want to know what these terms represent not the value. > > > > Thanking you > > Anik > > > > > > > > > > > > *** STK-14 Uppsala *** https://sites.google.com/site/stkmuu14/ > > Dr. Anik Sen, > > Post Doctoral Fellow, > > Ångströmlaboratoriet- Uppsala Universitet > > Box 538 > > SE-751 21 Uppsala > > Sweden > > Phone no:- +46-722781705 > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Equilibration from Non-shifted to Shifted Potential
Hi, Try it and see ;-) mdrun -nsteps 10 -reprod -deffnm shifted mdrun -nsteps 10 -reprod -deffnm not-shifted gmx check -f shifted -f2 not-shifted gmx check -e shifted -e2 not-shifted Alternatively, given that the forces are not computed from the energies (e.g. by central difference or some such), what role does the potential energy play in the integration scheme? :-) Mark On Fri, Nov 14, 2014 at 3:19 PM, Johnny Lu wrote: > Hi. > > If I change my potential from non-shifted to shift, will the sudden change > of energy from non-shifted to shifted potential at step 0 completely mess > up the equilibration? > > Thanks again. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Equilibration from Non-shifted to Shifted Potential
On Fri, Nov 14, 2014 at 3:51 PM, Johnny Lu wrote: > I guess I get the idea now. F = -dV(x)/dx. So no time derivative is > involved. So shifting the potential would not cause a suddenly impulse on > the system. > > By the way, is Potential-shift the default vdw and coulomb-modifier (so > that is used even if i didn't specify a modifier) for gromacs 4.6.7? > I didn't see the default value when I searched for vdw-modifier (p.214) of > gromacs manual 4.6.7, or when I look at the online manual. > >coulomb-modifier = Potential-shift >rcoulomb-switch = 0 >rcoulomb = 1 >vdwtype = Cut-off >vdw-modifier = Potential-shift > Indeed, seems we don't document that default (and we should). I forget what it is (but it is probably potential-shift-verlet). You can find out what it is by commenting those lines out of your input .mdp, and observing what grompp fills into the mdout.mdp. Mark > On Fri, Nov 14, 2014 at 9:31 AM, Mark Abraham > wrote: > > > Hi, > > > > Try it and see ;-) > > > > mdrun -nsteps 10 -reprod -deffnm shifted > > mdrun -nsteps 10 -reprod -deffnm not-shifted > > gmx check -f shifted -f2 not-shifted > > gmx check -e shifted -e2 not-shifted > > > > Alternatively, given that the forces are not computed from the energies > > (e.g. by central difference or some such), what role does the potential > > energy play in the integration scheme? :-) > > > > Mark > > > > > > On Fri, Nov 14, 2014 at 3:19 PM, Johnny Lu > wrote: > > > > > Hi. > > > > > > If I change my potential from non-shifted to shift, will the sudden > > change > > > of energy from non-shifted to shifted potential at step 0 completely > mess > > > up the equilibration? > > > > > > Thanks again. > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > posting! > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > * For (un)subscribe requests visit > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > > send a mail to gmx-users-requ...@gromacs.org. > > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Building executable for template.c!
On Sun, Nov 16, 2014 at 1:06 PM, Anjaiah Nalaparaju wrote: > Dear Users, > > I want to have executable file for template.c, but not in the default > location and not during the installation of whole package. I am trying to > do this for gromacs-4.6.5. > > When I use > > $cd /home/user/Documents/ > > $ tar xfz gromacs-4.6.5.tgz > $ cd gromacs-4.6.5 > $ mkdir build > $ cd build > $ cmake .. -DGMX_MPI=ON -DGMX_GPU=OFF -DGMX_BUILD_OWN_FFTW=ON > -DGMX_DEFAULT_SUFFIX=ON -DGMX_DOUBLE=ON > -DCMAKE_INSTALL_PREFIX=/home/user/gromacs4.6.5/ > > $ make install > > It installs gromacs package at /home/user/gromacs4.6.5/ and executable > for template.c is at > /home/user/Documents/gromacs4.6.5/build/share/template/. > > What I want to do is, I want to build the executable file for template > not during the installation of whole package. > That's good, because you can't do the alternative. The template is designed for use from the installation... > I have copied the folder "template"distribution directory as > /home/user/Documents/template/. Now I want to build the template using > the already installed gromacs. > > I have renamed the CMakeLists.txt.template to CMakeLists.txt. Then did > source /home/user/gromacs4.6.5/bin/GMXRC.bash. When I used cmake to > build executable I end-up with either of the following error. > ... so don't do this, get your stuff from /where/you/installed/share/gromacs/template where (e.g.) that renaming (and any interpolation required) are already handled (though IIRC there's none of the latter for 4.6). > -- checking for module 'libgmx_d' > -- package 'libgmx_d' not found > CMake Error at > /usr/local/share/cmake-2.8/Modules/FindPackageHandleStandardArgs.cmake:108 > (message): > Could NOT find GROMACS (missing: GROMACS_LIBRARY GROMACS_INCLUDE_DIR) > > or > > Could not find a package configuration file provided by "GROMACS" with > any > of the following names: > > GROMACSConfig.cmake > gromacs-config.cmake > > Add the installation prefix of "GROMACS" to CMAKE_PREFIX_PATH or set > "GROMACS_DIR" to a directory containing one of the above files. If > "GROMACS" provides a separate development package or SDK, be sure it has > been installed. > > Can anyone please guide me to build the executable for template.c in > the different place using the already installed gromacs package. I > think for the gromacs.4.5 this procedure is bit straight forward > > by changing the Makefile we can get it. But for gromacs-4.6.5 seems > not so straight forward. > There's a README in the template folder that suggests you source GMXRC. IIRC the template depends on pkg-config and source GMXRC is the main way to make that work. Mark Thanks in advance for your time and help. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] fitting problem
On Sun, Nov 16, 2014 at 9:08 PM, Rohit Farmer wrote: > Hi there, > > I am trying to fit a protein to a reference structure using the command > below > > trjconv -s run.trp -f run.xtc -o run-fit.xtc -fit progressive > Please copy and paste your actual command. Not what you think it was + typos + whatever changes you don't think matter :-). > > I am using protein for least square and system for output. > > This command always worked for me but for this particular protein the side > chains get crooked. I don't know how to explain but they look like flat > structures with random bonds between the atoms. > So take a screenshot, upload to a file-sharing service and share the link. > I tried -pbc mol and whole instead of fit just to get rid of the pbc effect > and don't care about fitting. But it also gave the same result. > Then you may be trying to fit files whose topology atom ordering does not match, or something like that. Note that if the molecules aren't whole in the .tpr file, then you won't be doing anything useful with some of the -pbc options. Mark > Can someone please help. > > Thanks > > Rohit > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] getting illegal instruction error in gromacs 4.6.4 execution
Hi, Have you read http://www.gromacs.org/Documentation/Installation_Instructions_4.6#4.3.1._Portability_aspects ? Mark On Mon, Nov 17, 2014 at 12:46 PM, Chaitali Chandratre wrote: > Dear Sir, > > Gromacs installation is giving illegal instruction error in job run. > > I have recompiled it using sse2...earlier it was with avx..and giving error > on particular nodes.. > but after recompilation also getting same error.. > > I am compiling with intel compilers. > > What steps shall I take further? > > Thanks in advance... > > -- > With Regards, >Chaitali > > "I know everything happens for a reason...But sometimes I wish I knew what > the reason was !! " > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
