Re: [gmx-users] Two ligands - One CPU ?

[jkrieger]

Hi Julian,

You can't send attachments to this list. Please upload the log file
somewhere and provide a link.

Best wishes
James

> Dear Gromacs Users,
>
> I have a very strange problem that I have not seen before: I am running
> three simulations of three crystal structures. It is the same protein
> bound
> to different ligands - in one case the ligand is two times present in the
> protein. All preparation steps and commands were exactly the same.
>
> When running the md simulation, strangely the protein with the two ligands
> is running only on one CPU while the other two simulations run on several
> CPUs. Has anybody experienced something like this before?
>
> I am also attaching the log file but I didn't see anything that looked
> suspicious to me.
>
> Thank you for your answers.
> Julian
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Re: [gmx-users] Is .mdp file are same for each force field?

[jkrieger]

Hi Chintan,

1. No, all forcefields have different parameters that you need to take
into account in your .mdp files, especially non-bonded cut-offs such as
rlist and rvdw, which are an integral part of the forcefield. Certainly
you need to use a forcefield that includes zinc if you have zinc in your
protein (that said the error could also be that zinc is present but not be
called ZN in some forcefields). You can get bits of mdp files that are
forcefield-specific on the gromacs website e.g.
http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM - you
can remove the /CHARMM and get a page to click through others.

2. Any mdp with constant temperature would need changing i.e. nvt.mdp,
npt.mdp and md.mdp - you should really read through the mdp files and
understand what's going on. Also look at
http://manual.gromacs.org/online/mdp_opt.html and there are options
related to temperature coupling. You may want to equilibrate to higher
temperature in steps by copying nvt.mdp and changing each one to have
progressively higher values.

Best wishes
James

> Dear gromacs user,
>
> I practiced of MD stimulation with LysoZyme tutorial. Now, They used 15:
> OPLS-AA/L force field and also i saved all *.mdp* file (ions. mdp, md.mdp,
> nvt.mdp, npt.mdp, minim.mdp, etc.) as given in tutorial and successfully
> performed MD stimulation.
>
> Now, I have want to study my protein. I found force field 9 to 14 are
> reported for my protein in literature. Further, I also tried it and found
> "Residue 'ZN' not found in residue topology database" only for force field
> 15 (OPLS-AA/L force field), not for any other force field (9 to 14).
>
>
>
> *Now, I have two questions.*
>
> *1) Can i use this file for stimulation study with other force field (9 to
> 14)? If not, from where i get them?*
> *2) Also want to study MD at higher temperature, still Can i use tutorial
> .mdp files? or what informations i have to change in files (.mdp)*
>
> Can any one tell me what to do?
>
>
> --
> Regards,
> Chintan Bhagat
> Research scholar,
> V.N.S.G.U, India
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Re: [gmx-users] DETECTING HYDROGEN BONDS

[jkrieger]

I think the 2nd column is the number of hydrogen bonds based on distance
and angle whereas the 3rd column is all pairs within the 0.35 nm distance
cutoff ignoring angles. This is stated by the lines

@ s0 legend "Hydrogen bonds"
@ s1 legend "Pairs within 0.35 nm"

Best wishes
James

> Thank you very much for the reply
>
>
> Wanted to know what the third column represents?
>
>
> The header was
>
>
> # gmx hbond is part of G R O M A C S:
> # # Glycine aRginine prOline Methionine Alanine Cystine Serine #
> @title "Hydrogen Bonds"
> @xaxis  label "Time (ps)"
> @yaxis  label "Number"
> @TYPE xy @ view 0.15, 0.15, 0.75, 0.85
> @ legend on @ legend box on
> @ legend loctype view
> @ legend 0.78, 0.8
> @ legend length 2
> @ s0 legend "Hydrogen bonds"
> @ s1 legend "Pairs within 0.35 nm"
>
> Through molecular docking had obtained hydrogen bonding with GLU 387 AND
> GLU 389
>
> Wish to ascertain them through simulations too. How to do it?
>
> Thanks,
> Subashini.K
>
>
>
>
>
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
>  on behalf of Alex
> 
> Sent: Saturday, February 11, 2017 1:45 PM
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] DETECTING HYDROGEN BONDS
>
> Not sure what you mean by "interpret these numbers," except that now we
> know that your simulation was 2 ns long.  The xvg file contains a
> header, which describes what each column is. If I recall correctly, the
> second column is the number of hbonds according to the default search
> cutoff. The first column is your simulated time in ps.
>
> Alex
>
>
> On 2/11/2017 1:00 AM, Subashini .K wrote:
>> Hi gromacs users,
>>
>>
>> After protein ligand simulations, gave the following command to detect
>> hydrogen bond
>>
>>
>> gmx hbond -f npt.trr -s npt.tpr -num hbond.xvg
>>
>> After selecting protein and ligand
>>
>>
>> Obtained the following result
>>
>>
>> I am a beginner. Could someone help me  to interpret these numbers? The
>> simulation was done for 2 ns
>>
>>
>>
>>  0   2   1
>>
>>100   2   1
>>
>> 200   1   0
>>
>> 300   1   0
>>
>> 400   1   0
>>
>> 500   1   0
>>
>> 600   1   0
>>
>>700   1   0
>>
>>800   0   0
>>
>>900   1   0
>>
>> 1000   1   0
>>
>>  1100   1   0
>>
>>   1200   1   0
>>
>>   1300   0   2
>>
>>  1400   1   0
>>
>>   1500   1   0
>>
>>   1600   1   0
>>
>>1700   1   0
>>
>>   1800   0   1
>>
>>1900   1   0
>>
>>   2000   1   0
>>
>>
>> Thanks,
>>
>> Subashini.K
>
>
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Re: [gmx-users] Plumed with GROMACS 5.1.2

[jkrieger]

Hi Amit,

You patch plumed onto the gromacs source and then yes you need to
recompile gromacs. It may help to look at this thread from the plumed
google group
https://groups.google.com/forum/#!topic/plumed-users/stlK9-kaa6A where I
worked out how to do it. I was using plumed 2.1 which had some problems
that should be fixed in 2.3 I think so you definitely don't need to add
the -fPIC flag and probably don't need to remove the duplicate reference
to Plumed.o

Best wishes
James

> Hello,
> I have installed plumed 2.3. But I am having doubt in the patching
> process.
> Where should I patch the executable? Do I need to recompile gromacs after
> patching ?
>
> Thanks
> Amit Behera
>
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Re: [gmx-users] GMX-PLUMED speed

[jkrieger]

Interesting finding. Have you tried leaving out the two options
independently? Also would be good to try that with gromacs-2016.

What is your system size and cluster usage? This sounds a phenomenal speed
as well as speed up.

You should probably share this on the plumed google group too.

Best wishes
James

>
> Dears,
>
> I am using gromacs v5.1.4 with PLUMED v2.3.0.
>
> Through my experience as a novice in using PLUMED, I have noticed that not
> writing the restraint/forces info in a file and not using a STRIDE
> accelerate the code significantly.
>
> Using a line such as follows in the plumed parameters set:
> PRINT ARG=restraint.bias
>
> instead of the most correct:
> PRINT STRIDE=1 ARG=restraint.bias FILE=bias
>
> would make gmx run at 950 ns/day instead of 550 ns/day.
>
> The inconvenient is that the log file becomes large (all the restraint are
> written in it) and messy (the values are mixing with the rest of the info
> on exchanges), but the speed up is considerable.
>
> Note that I still print the values of the restraint in a file, which I
> haven’t tried to remove but it could also speed up the run.
>
> Someone should may be look at this as he speed up applies on XX replicas
> so lots of CPU time (cooling system, energy, climat change, …) is
> wasted.
>
> I hope this helps.
> X-
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Re: [gmx-users] Dynamics

[jkrieger]

No, that's wrong because the box does not exist for the protein and water,
they exist in an infinite lattice so the protein outside the box goes into
the next box and interacts with the water there. This is the same as
interacting with water on the other side of the same box, which is how
it's treated in the simulation calculations.

> Thank you
>
> But if I am extending my simulation with protein outside the box, then
> there will not be any effect of water molecules right.?
>
>
> On Thu, 26 Jan 2017 at 1:25 PM,  wrote:
>
>> Hi Rahul,
>>
>>
>>
>> The protein being out of the box is not a problem except for
>> visualisation
>>
>> and some analysis (e.g. RMSD). For continuing the simulation, it is a
>>
>> completely normal consequence of having periodic boundaries and you
>>
>> shouldn't worry about it. You can then fIx the protein for visualisation
>>
>> and analysis separately to running. See
>>
>>
>> http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
>>
>>
>>
>> To continue the simulation just use mdrun as normal but with the -cpi
>>
>> flag. If you want more time than you originally set the mdp to ask for
>>
>> then use tpbconv (gmx convert_tpr in gromacs 5 and later). See
>>
>> http://www.gromacs.org/Documentation/How-tos/Extending_Simulations
>>
>>
>>
>> Best wishes
>>
>> James
>>
>>
>>
>> > Hi mark
>>
>> >
>>
>> > I want to extend it for another 50ns. At 100ns protein is out of the
>> box.
>>
>> > Now is t possible to apply boundary conditions and extend.?
>>
>> >
>>
>> >
>>
>> >
>>
>> > On Wed, 25 Jan 2017 at 11:12 PM, Mark Abraham
>> 
>>
>> > wrote:
>>
>> >
>>
>> >> Hi,
>>
>> >>
>>
>> >>
>>
>> >>
>>
>> >> On Wed, 25 Jan 2017 18:00 RAHUL SURESH 
>> wrote:
>>
>> >>
>>
>> >>
>>
>> >>
>>
>> >> > from production output of a monomer for 100ns, there s a
>> instability
>>
>> >> in
>>
>> >> the
>>
>> >>
>>
>> >> > structure from 83ns to 100ns.
>>
>> >>
>>
>> >>
>>
>> >>
>>
>> >>
>>
>> >>
>>
>> >> Many things could be going on here...
>>
>> >>
>>
>> >>
>>
>> >>
>>
>> >> Also .gro file shows, the protein is out of
>>
>> >>
>>
>> >> > the cube.
>>
>> >>
>>
>> >> >
>>
>> >>
>>
>> >>
>>
>> >>
>>
>> >> Mdrun doesn't care. There's infinitely many equivalent
>> representations
>>
>> >> of a
>>
>> >>
>>
>> >> periodic system.
>>
>> >>
>>
>> >>
>>
>> >>
>> http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
>>
>> >>
>>
>> >>
>>
>> >>
>>
>> >>
>>
>> >>
>>
>> >> > gmx make_ndx -f md.gro -o index.ndx
>>
>> >>
>>
>> >> > trjconv -f md.xtc -s md.tpr -n index.ndx -pbc mol -ur compact
>> -center
>>
>> >> -o
>>
>> >>
>>
>> >> > outputfile.xtc
>>
>> >>
>>
>> >> >
>>
>> >>
>>
>> >> > I used the above commands to bring the protein to the center of the
>>
>> >> box.
>>
>> >>
>>
>> >> >
>>
>> >>
>>
>> >> > gmx trjconv -f outputfile.xtc -s md.tpr -o newmd.trr
>>
>> >>
>>
>> >> >
>>
>> >>
>>
>> >> > And using the above command, extracted a trr file.
>>
>> >>
>>
>> >> >
>>
>> >>
>>
>> >> > Now can I extend this job with this trr file as it is or should i
>> give
>>
>> >> any
>>
>> >>
>>
>> >> > periodic boundary conditions or should take the conformer structure
>> at
>>
>> >> 80ns
>>
>> >>
>>
>> >> > and run for another 50ns?
>>
>> >>
>>
>> >> >
>>
>> >>
>>
>> >>
>>
>> >>
>>
>> >> None of this is needed. See
>>
>> >>
>>
>> >> http://www.gromacs.org/Documentation/How-tos/Extending_Simulations
>>
>> >>
>>
>> >>
>>
>> >>
>>
>> >> Whether it makes sense to try to repeat or extend or go back to the
>>
>> >> start
>>
>> >>
>>
>> >> and try to fix something depends on what the "instability" is, and
>> what
>>
>> >> is
>>
>> >>
>>
>> >> causing it.
>>
>> >>
>>
>> >>
>>
>> >>
>>
>> >> Mark
>>
>> >>
>>
>> >>
>>
>> >>
>>
>> >> waiting for your valuable note.
>>
>> >>
>>
>> >> > --
>>
>> >>
>>
>> >> > *Regards,*
>>
>> >>
>>
>> >> > *Rahul Suresh*
>>
>> >>
>>
>> >> > *Research Scholar*
>>
>> >>
>>
>> >> > *Bharathiar University*
>>
>> >>
>>
>> >> > *Coimbatore*
>>
>> >>
>>
>> >> > --
>>
>> >>
>>
>> >> > 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
>>
>> >>
>>
>> >>
>>
>> >>
>>
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>>
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>>
>> >> posting!
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Re: [gmx-users] Dynamics

[jkrieger]

Hi Rahul,

The protein being out of the box is not a problem except for visualisation
and some analysis (e.g. RMSD). For continuing the simulation, it is a
completely normal consequence of having periodic boundaries and you
shouldn't worry about it. You can then fIx the protein for visualisation
and analysis separately to running. See
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

To continue the simulation just use mdrun as normal but with the -cpi
flag. If you want more time than you originally set the mdp to ask for
then use tpbconv (gmx convert_tpr in gromacs 5 and later). See
http://www.gromacs.org/Documentation/How-tos/Extending_Simulations

Best wishes
James

> Hi mark
>
> I want to extend it for another 50ns. At 100ns protein is out of the box.
> Now is t possible to apply boundary conditions and extend.?
>
>
>
> On Wed, 25 Jan 2017 at 11:12 PM, Mark Abraham 
> wrote:
>
>> Hi,
>>
>>
>>
>> On Wed, 25 Jan 2017 18:00 RAHUL SURESH  wrote:
>>
>>
>>
>> > from production output of a monomer for 100ns, there s a instability
>> in
>> the
>>
>> > structure from 83ns to 100ns.
>>
>>
>>
>>
>>
>> Many things could be going on here...
>>
>>
>>
>> Also .gro file shows, the protein is out of
>>
>> > the cube.
>>
>> >
>>
>>
>>
>> Mdrun doesn't care. There's infinitely many equivalent representations
>> of a
>>
>> periodic system.
>>
>>
>> http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
>>
>>
>>
>>
>>
>> > gmx make_ndx -f md.gro -o index.ndx
>>
>> > trjconv -f md.xtc -s md.tpr -n index.ndx -pbc mol -ur compact -center
>> -o
>>
>> > outputfile.xtc
>>
>> >
>>
>> > I used the above commands to bring the protein to the center of the
>> box.
>>
>> >
>>
>> > gmx trjconv -f outputfile.xtc -s md.tpr -o newmd.trr
>>
>> >
>>
>> > And using the above command, extracted a trr file.
>>
>> >
>>
>> > Now can I extend this job with this trr file as it is or should i give
>> any
>>
>> > periodic boundary conditions or should take the conformer structure at
>> 80ns
>>
>> > and run for another 50ns?
>>
>> >
>>
>>
>>
>> None of this is needed. See
>>
>> http://www.gromacs.org/Documentation/How-tos/Extending_Simulations
>>
>>
>>
>> Whether it makes sense to try to repeat or extend or go back to the
>> start
>>
>> and try to fix something depends on what the "instability" is, and what
>> is
>>
>> causing it.
>>
>>
>>
>> Mark
>>
>>
>>
>> waiting for your valuable note.
>>
>> > --
>>
>> > *Regards,*
>>
>> > *Rahul Suresh*
>>
>> > *Research Scholar*
>>
>> > *Bharathiar University*
>>
>> > *Coimbatore*
>>
>> > --
>>
>> > 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
>>
>>
>>
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>>
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Re: [gmx-users] VMD

[jkrieger]

Hi Rahul,

VMD ran out of memory. Try using trjconv to create a new xtc with a subset
of atoms or a subset of frames.

Best wishes
James

> I tried to visualize my xtc on VMD and the job get killed at 7000 frames
>
> why is that so?
>
> --
> *Regards,*
> *Rahul Suresh*
> *Research Scholar*
> *Bharathiar University*
> *Coimbatore*
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Re: [gmx-users] parallel processing

[jkrieger]

Hi Abhisek,

You would need to use another version of gromacs with mpi rather than
thread-mpi (installed by adding DGMX_MPI=ON to the cmake command). You
could then use the following command

mpirun -np 4 gmx_mpi mdrun -ntomp 16 -npme 0 -v -deffnm em

I'm not sure why you are specifying -npme 0 but would suggest you don't do
this and instead let the number of separate pme ranks be set
automatically.

Best wishes
James

> Hi,
>
> I'm running gromacs on a cluster configuration as follows:
> 1 node = 16 cores
>
> I'm able to use single node with "gmx mdrun -ntmpi 4 -ntomp 16 -npme 0 -v
> -deffnm em" command.
>
> How can I be able to run on multiple node (I have 20 nodes available) ?
> "-nt" is not doing good here.
>
>
>
> --
> Abhisek Mondal
>
> *Research Fellow*
>
> *Structural Biology and Bioinformatics Division*
> *CSIR-Indian Institute of Chemical Biology*
>
> *Kolkata 700032*
>
> *INDIA*
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Re: [gmx-users] Tutorials to apply NMR data on Gromacs calculations of protein struture

[jkrieger]

Hi Kat,

You can do this using Plumed patched onto Gromacs. There's a tutorial for
this at https://plumed.github.io/doc-v2.3/user-doc/html/belfast-9.html

Best wishes
James

> Hi All,
>
> I would like to combine NMR study (specifically relaxation data, RDC and
> dihedral restraints) with Gromacs calculations to study possible ensembles
> of protein structure.
>
> I tried to search NMR refinement by Gromacs but could not see any tutorial
> for this purpose, except one with distance restraints (but we did not have
> good NOE data to try). Could anyone help me where can I learn to perform
> NMR refinement with Gromacs.
>
> Thanks
> Kat
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Re: [gmx-users] Difference between POPI and DOPI membranes? and about lipid headgroups

[jkrieger]

You're welcome.

> Dear James,
>
> Thank you very much for your helpful suggestion.
>
> Best regards,
>
>
>
> Message: 3
> Date: Wed, 19 Oct 2016 22:57:15 +0100
> From: jkrie...@mrc-lmb.cam.ac.uk
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Difference between POPI and DOPI membranes?
> and about lipid headgroups
> Message-ID:
> 
> Content-Type: text/plain
>
> My suggestion is to mix and match parameters to extend from overlapping
> regions. I did that to model GABA from glutamate and lysine. I just found
> this thread via a google search that suggests DOPC and POPI
> http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2014-2015/2406.html
>
> Best wishes
> James
>
>> Dear gmx users,
>>
>> I would like to simulate DOPI membrane system. I could not find DOPI
>> membrane model from Charmm-gui, and I read that the closest one is POPI
>> bilayer. I checked atoms of the lipids. First, there are carbons end of
>> one
>> tail needed to DOPI. Second, I need to change bond type from double to
>> single in the middle of two tails.* (1) *Can I use the parameters of the
>> POPI for DOPI membrane?
>>
>> In the head groups (PO4), there is a protonated oxygen in DOPI membrane
>> figure. *(2).* Can I use deprotonated head group for my simulations?
>>
>> Please, suggest and advice me?
>>
>>
>> Best regards,
>>
>> Mijiddorj
>> --
> --
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Re: [gmx-users] Difference between POPI and DOPI membranes? and about lipid headgroups

[jkrieger]

My suggestion is to mix and match parameters to extend from overlapping
regions. I did that to model GABA from glutamate and lysine. I just found
this thread via a google search that suggests DOPC and POPI
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2014-2015/2406.html

Best wishes
James

> Dear gmx users,
>
> I would like to simulate DOPI membrane system. I could not find DOPI
> membrane model from Charmm-gui, and I read that the closest one is POPI
> bilayer. I checked atoms of the lipids. First, there are carbons end of
> one
> tail needed to DOPI. Second, I need to change bond type from double to
> single in the middle of two tails.* (1) *Can I use the parameters of the
> POPI for DOPI membrane?
>
> In the head groups (PO4), there is a protonated oxygen in DOPI membrane
> figure. *(2).* Can I use deprotonated head group for my simulations?
>
> Please, suggest and advice me?
>
>
> Best regards,
>
> Mijiddorj
> --
> Gromacs Users mailing list
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> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
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Re: [gmx-users] trr file

[jkrieger]

Hi Rita,

You should be able to use analysis tools on an xtc file instead.
Storage-wise you could also just have an xtc. For restarting if any files
are missing they should all be missing except the cpt. You can rename or
move the rest rather than deleting them though.

Best wishes
James

> Dear all,
>
> Probably a rookie question but anyone knows how to reduce trajectory
> volume file to be analyzed (I have already tried trjconv)? I have a trr
> file with  167 GB and analysis tools crash.
>
> Thanks,
> Rita.
>
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Re: [gmx-users] Fwd: Questions for the forum

[jkrieger]

You probably want to use -box 1.2 1.2 1.2 rather than -d 1.2.

Best wishes
James

> Thank you Mark, will look into that!
>
> 2016-10-13 15:45 GMT+01:00 Mark Abraham :
>
>> Hi,
>>
>> Do check out gmx editconf -h for what it says about -d. Hint, that isn't
>> setting the box dimensions directly, which is why you're getting a much
>> bigger box.  Look also at the output of editconf, which will tel lyou
>> that
>> it's too big.
>>
>> Mark
>>
>> On Thu, Oct 13, 2016 at 4:39 PM Matilde Viegas
>> 
>> wrote:
>>
>> > I started with a pdb file of the protein, 5000 residues, no solvent,
>> > crystallographic structure.
>> >
>> > Generated the .gro file, opting for the AMBER99SB force field (option
>> 5):
>> >
>> > gmx pdb2gmx -f YYY.pdb -o YYY_GROMACS.gro -water tip3p -ignh (opted
>> > for ignh as I was having trouble with differences in nomemclature)
>> >
>> > defined box:
>> >
>> > gmx editconf -f YYY_GROMACS.gro -o YYY_newbox.gro -c -d 1.2 -bt
>> > dodechaedron
>> >
>> > solvation:
>> >
>> > gmx solvate -cp YYY_GROMACS_newbox.gro -cs spc216.gro -o
>> > YYY_GROMACS_newboxsolv.gro -p topol.top
>> >
>> > add ions:
>> >
>> > gmx grompp -f ions.mdp -c YYY_newboxsolv.gro -p topol.top -o ions.tpr
>> >
>> > gmx genion -s ions.tpr -o YYY_newboxsolv_ions.gro -p topol.top -pname
>> > NA -np 76 (the charge was -76)  (chose group 13 like the tutorial,
>> > SOL)
>> >
>> >
>> > at this point, my topol is:
>> > [ molecules ]
>> > ; Compound#mols
>> > Protein_chain_X 1
>> > SOL 766582
>> > NA   76
>> >
>> > and from this point i went on with minimization and so on.
>> >
>> >
>> >
>> > 2016-10-13 14:49 GMT+01:00 Justin Lemkul :
>> >
>> > >
>> > >
>> > > On 10/13/16 9:45 AM, Matilde Viegas wrote:
>> > >
>> > >> Of course, sorry!
>> > >> I followed your lyzosyme tutorial, the exact same commands, only
>> > addapting
>> > >> it to my system (force field, tip3p water, just like I did on
>> AMBER),
>> > box
>> > >> was dodechaedron, 1.2nm. I didn't alter anything beside that... My
>> > enzyme
>> > >> is around 72 thousand atoms, after adding the solvation box, it
>> goes
>> up
>> > to
>> > >> 2.5 million atoms.
>> > >>
>> > >>
>> > > You need to provide your exact commands, copied and pasted from the
>> > > terminal. You can't just say you did my tutorial, because there's a
>> lot
>> > of
>> > > differences in what you actually did and what's in that example.
>> > >
>> > > One thing that is unclear is if you're trying to import an
>> > > already-solvated system from AMBER into GROMACS.  If you are, then
>> you
>> > > shouldn't be re-sizing the box or adding any more water.  But again,
>> only
>> > > your exact commands and descriptions of file contents will tell us
>> > anything
>> > > productive.
>> > >
>> > > -Justin
>> > >
>> > >
>> > > 2016-10-13 14:40 GMT+01:00 Justin Lemkul :
>> > >>
>> > >>
>> > >>>
>> > >>> On 10/13/16 9:38 AM, Matilde Viegas wrote:
>> > >>>
>> > >>> Yes, I noticed that! I said 10, referring to angstrom, in the
>> input I
>> > had
>> >  1.0nm.
>> > 
>> >  So you probably think it is only some error in the input, not
>> really
>> >  something I can tackle, right? I really can't figure it out...
>> > 
>> > 
>> >  Without seeing your exact sequence of commands, there's nothing
>> we
>> can
>> > >>> do
>> > >>> to help.  The only thing consistent with having an unexpected
>> > >>> million-atom
>> > >>> system is that you set up the box incorrectly with editconf.  But
>> you
>> > >>> haven't told us exactly what you've done...
>> > >>>
>> > >>> -Justin
>> > >>>
>> > >>>
>> > >>> Thank you for your time, Justin
>> > >>>
>> > 
>> >  2016-10-13 13:04 GMT+01:00 Justin Lemkul :
>> > 
>> > 
>> > 
>> > > On 10/13/16 7:34 AM, Matilde Viegas wrote:
>> > >
>> > > I tried to downzise to 10 and yet the reduction was very little.
>> I
>> > was
>> > >
>> > >> just
>> > >> trying t understand how can the difference between the same
>> systems,
>> > >> using
>> > >> either AMBER or GROMACS, can be of 1 million atoms...
>> > >>
>> > >>
>> > >> GROMACS uses SI units, so distances/box vectors are specified
>> in
>> nm,
>> > >> not
>> > >>
>> > > Angstrom.  See Chapter 2 of the manual for unit conventions.
>> > >
>> > > -Justin
>> > >
>> > >
>> > > 2016-10-13 12:27 GMT+01:00 Dd H :
>> > >
>> > >
>> > >> You can reduce your box size to get a smaller system.
>> > >>
>> > >>
>> > >>> On 13 October 2016 at 17:41, Matilde Viegas <
>> > >>> matildefrvie...@gmail.com
>> > >>>
>> > 
>> >  wrote:
>> > >>>
>> > >>> Hi,
>> > >>>
>> > >>>
>> >  my name is Matilde. This is my first time using GROMACS. I'm
>> >  switching
>> > 
>> >  from
>> > 
>> > >>>
>> > >>> AMBER to GROMACS however I'm having some trouble reproducing
>> my
>> > >>> system:
>> > >>>
>> > 
>> > >>>

Re: [gmx-users] Different Results with Different Platforms

[jkrieger]

That is not a bug. The idea of NVT is it keeps your volume constant not
your pressure. In theory the pressure should stay fairly constant for a
given temperature as the solvent pushes against the boundaries or itself
to a fairly constant extent that depends on its velocities. I have not
however heard of anyone usually pressure coupling (NPT) for equilibration
only but I imagine it should work. You'd probably be best to keep the
velocities to be sure rather than generating them again. Did you not use
the same mdp files in the same order on all machines?

Best wishes
James

> As advised, I compared the systems between the different platforms and
> found the bug.
> I had initially equilibrated the pressure of my system in an NPT run
> before
> doing an NVT run on my desktop.
> Unbeknownst to me,  editconf had adjusted the coordinates of my molecules
> such that the pressure during the NVT run was almost 3 orders of magnitude
> higher than the initially equilibrated pressure, hence the unusual
> behaviour.
> I just did an NPT run on my desktop and it is loooking good.
> This bug cost me some frustrating weeks of my life but on the bright side,
> I may just get a publication from studying  it. :D
>
> Thank you so, so much Mark, Justin and Szilárd.
> I really appreciate your assistance!
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Re: [gmx-users] Running Gromacs in parallel

[jkrieger]

Thanks again

> On Wed, Sep 21, 2016 at 9:55 PM,   wrote:
>> Thanks Sz.
>>
>> Do you think going up to from version 5.0.4 to 5.1.4 would really make
>> such a big difference?
>
> Note that I was recommending using a modern compiler + the latest
> release (which is called 2016 not 5.1.4!). It's hard to guess the
> improvements, but from 5.0->2016 you should see double-digit
> percentage improvements and going from gcc 4.4 to 5.x or 6.0 wil also
> have a significant improvement.

I was still thinking of 2016 as too new to be used for simulations I might
want to publish. I will try it when I can then.

>
>> Here is a log file from a single md run (that has finished unlike the
>> metadynamics) with the number of OpenMP threads matching how many
>> threads
>> there are on each node. This has been restarted a number of times with
>> different launch configurations being mostly the number of nodes and the
>> node type (either 8 CPUs or 24 CPUs).
>> https://www.dropbox.com/s/uxzsj3pm31n66nz/md.log?dl=0
>
> You seem to be using a single MPI rank per node ion these runs. That
> will almost never be optimal, especially not when DD is not limited.

Yes, I only realised that recently and I thought it might be useful to see
this log seeing as it is a complete run and has the bit at the bottom.
Here is a multiple walker metadynamics log, includes some other
combinations I tried.

https://www.dropbox.com/s/td7ps45dzz1otwz/from_cluster_metad0.log?dl=0

>
>> From timesteps when checkpoints were written I can see that these
>> configurations make quite a difference and per CPU, having 8 OpenMP
>> threads per MPI process becomes a much worse idea stepping from 4 nodes
>> to
>> 6 nodes, i.e. having more CPUs makes mixed paralellism less favourable
>> as
>> suggested in figure 8. Yes, the best may not lie at 1 OpenMP thread per
>> MPI rank and may vary depending on the number of CPUs as well.
>
> Sure, but 8 threads panning over two sockets will definitely be
> suboptimal. Start with trying fewer and consider using separate PME
> ranks especially if you have ethernet.

ok

>
>> Also, I can
>> see that for the same number of CPUs, the 24-thread nodes are better
>> than
>> the 8-thread nodes but I can't get so many of them as they are also more
>> popular for RELION users.
>
> FYI those are 2x6-core CPUs with Hyperthreading, so 2x12 hardware
> threads. Also the two generations newer, so it's not surprising that
> they are much faster. Still, 24 threads/node is too much. Use less.
>
>> What can I infer from the information at the
>> end?
>
> Before starting to interpret that, it's worth fixing the above issues ;)
> Otherwise, what's clear is that PME is taking a considerable amount of
> time, especially given the long cut-off.
>
> Cheers,
> --
> Szilárd
>
>
>>
>> Best wishes
>> James
>>
>>> Hi,
>>>
>>> On Wed, Sep 21, 2016 at 5:44 PM,   wrote:
 Hi Szilárd,

 Yes I had looked at it but not with our cluster in mind. I now have a
 couple of GPU systems (both have an 8-core i7-4790K CPU with one Titan
 X
 GPU on one system and two Titan X GPUs on the other), and have been
 thinking about about getting the most out of them. I listened to
 Carsten's
 BioExcel webinar this morning and it got me thinking about the cluster
 as
 well. I've just had a quick look now and it suggests Nrank = Nc and
 Nth
 =
 1 for high core count, which I think worked slightly less well for me
 but
 I can't find the details so I may be remembering wrong.
>>>
>>> That's not unexpected, the reported values are specific to the
>>> hardware and benchmark systems and only give a rough idea where the
>>> ranks/threads balance should be.

 I don't have log files from a systematic benchmark of our cluster as
 it
 isn't really available enough for doing that.
>>>
>>> That's not really necessary, even logs from a single production run
>>> can hint possible improvements.
>>>
 I haven't tried gmx tune_pme
 on there either. I do have node-specific installations of
 gromacs-5.0.4
 but I think they were done with gcc-4.4.7 so there's room for
 improvement
 there.
>>>
>>> If that's the case, I'd simply recommend using a modern compiler and
>>> if you can a recent GROMACS version, you'll gain more performance than
>>> from most launch config tuning.
>>>
 The cluster nodes I have been using have the following cpu specs
 and 10Gb networking. It could be that using 2 OpenMP threads per MPI
 rank
 works nicely because it matches the CPU configuration and makes better
 use
 of hyperthreading.
>>>
>>> Or because of the network. Or for some other reason. Again, comparing
>>> the runs' log files could tell more :)
>>>
 Architecture:  x86_64
 CPU op-mode(s):32-bit, 64-bit
 Byte Order:Little Endian
 CPU(s):8
 On-line CPU(s) list:   0-7
 Thread(s) per core:2
 Core(s) per socket:2
>>

Re: [gmx-users] Running Gromacs in parallel

[jkrieger]

Thanks Sz.

Do you think going up to from version 5.0.4 to 5.1.4 would really make
such a big difference?

Here is a log file from a single md run (that has finished unlike the
metadynamics) with the number of OpenMP threads matching how many threads
there are on each node. This has been restarted a number of times with
different launch configurations being mostly the number of nodes and the
node type (either 8 CPUs or 24 CPUs).
https://www.dropbox.com/s/uxzsj3pm31n66nz/md.log?dl=0

>From timesteps when checkpoints were written I can see that these
configurations make quite a difference and per CPU, having 8 OpenMP
threads per MPI process becomes a much worse idea stepping from 4 nodes to
6 nodes, i.e. having more CPUs makes mixed paralellism less favourable as
suggested in figure 8. Yes, the best may not lie at 1 OpenMP thread per
MPI rank and may vary depending on the number of CPUs as well. Also, I can
see that for the same number of CPUs, the 24-thread nodes are better than
the 8-thread nodes but I can't get so many of them as they are also more
popular for RELION users. What can I infer from the information at the
end?

Best wishes
James

> Hi,
>
> On Wed, Sep 21, 2016 at 5:44 PM,   wrote:
>> Hi Szilárd,
>>
>> Yes I had looked at it but not with our cluster in mind. I now have a
>> couple of GPU systems (both have an 8-core i7-4790K CPU with one Titan X
>> GPU on one system and two Titan X GPUs on the other), and have been
>> thinking about about getting the most out of them. I listened to
>> Carsten's
>> BioExcel webinar this morning and it got me thinking about the cluster
>> as
>> well. I've just had a quick look now and it suggests Nrank = Nc and Nth
>> =
>> 1 for high core count, which I think worked slightly less well for me
>> but
>> I can't find the details so I may be remembering wrong.
>
> That's not unexpected, the reported values are specific to the
> hardware and benchmark systems and only give a rough idea where the
> ranks/threads balance should be.
>>
>> I don't have log files from a systematic benchmark of our cluster as it
>> isn't really available enough for doing that.
>
> That's not really necessary, even logs from a single production run
> can hint possible improvements.
>
>> I haven't tried gmx tune_pme
>> on there either. I do have node-specific installations of gromacs-5.0.4
>> but I think they were done with gcc-4.4.7 so there's room for
>> improvement
>> there.
>
> If that's the case, I'd simply recommend using a modern compiler and
> if you can a recent GROMACS version, you'll gain more performance than
> from most launch config tuning.
>
>> The cluster nodes I have been using have the following cpu specs
>> and 10Gb networking. It could be that using 2 OpenMP threads per MPI
>> rank
>> works nicely because it matches the CPU configuration and makes better
>> use
>> of hyperthreading.
>
> Or because of the network. Or for some other reason. Again, comparing
> the runs' log files could tell more :)
>
>> Architecture:  x86_64
>> CPU op-mode(s):32-bit, 64-bit
>> Byte Order:Little Endian
>> CPU(s):8
>> On-line CPU(s) list:   0-7
>> Thread(s) per core:2
>> Core(s) per socket:2
>> Socket(s): 2
>> NUMA node(s):  2
>> Vendor ID: GenuineIntel
>> CPU family:6
>> Model: 26
>> Model name:Intel(R) Xeon(R) CPU   E5530  @ 2.40GHz
>> Stepping:  5
>> CPU MHz:   2393.791
>> BogoMIPS:  4787.24
>> Virtualization:VT-x
>> L1d cache: 32K
>> L1i cache: 32K
>> L2 cache:  256K
>> L3 cache:  8192K
>> NUMA node0 CPU(s): 0,2,4,6
>> NUMA node1 CPU(s): 1,3,5,7
>>
>> I appreciate that a lot is system-dependent and that I can't really help
>> you help me very much. It also should be noted that my multi runs are
>> multiple walker metadynamics run and are slowing down because there are
>> large bias potentials in memory that need to be communicated around too.
>> As I said I haven't had a chance to make separate benchmark runs but
>> have
>> just made observations based upon existing runs.
>
> Understandable, I was just giving tips and hints.
>
> Cheers,
> --
> Sz.
>
>
>> Best wishes
>> James
>>
>>> Performance tuning is highly dependent on the simulation system and
>>> the hardware you're running on. Questions like the ones you pose are
>>> impossible to answer meaningfully without *full* log files (and
>>> hardware specs including network).
>>>
>>> Have you checked the performance checklist I linked above?
>>> --
>>> SzilÃĄrd
>>>
>>>
>>> On Wed, Sep 21, 2016 at 11:36 AM,   wrote:
 I wonder whether what I see that -np 108 and -ntomp 2 is best comes
 from
 using -multi 6 with 8-CPU nodes. That level of parallelism may then be
 necessary to trigger automatic segregation of PP and PME ranks. I'm
 not
 sure if I tried -np 54 and -ntomp 4, which would proba

Re: [gmx-users] Running Gromacs in parallel

[jkrieger]

Hi Szilárd,

Yes I had looked at it but not with our cluster in mind. I now have a
couple of GPU systems (both have an 8-core i7-4790K CPU with one Titan X
GPU on one system and two Titan X GPUs on the other), and have been
thinking about about getting the most out of them. I listened to Carsten's
BioExcel webinar this morning and it got me thinking about the cluster as
well. I've just had a quick look now and it suggests Nrank = Nc and Nth =
1 for high core count, which I think worked slightly less well for me but
I can't find the details so I may be remembering wrong.

I don't have log files from a systematic benchmark of our cluster as it
isn't really available enough for doing that. I haven't tried gmx tune_pme
on there either. I do have node-specific installations of gromacs-5.0.4
but I think they were done with gcc-4.4.7 so there's room for improvement
there. The cluster nodes I have been using have the following cpu specs
and 10Gb networking. It could be that using 2 OpenMP threads per MPI rank
works nicely because it matches the CPU configuration and makes better use
of hyperthreading.

Architecture:  x86_64
CPU op-mode(s):32-bit, 64-bit
Byte Order:Little Endian
CPU(s):8
On-line CPU(s) list:   0-7
Thread(s) per core:2
Core(s) per socket:2
Socket(s): 2
NUMA node(s):  2
Vendor ID: GenuineIntel
CPU family:6
Model: 26
Model name:Intel(R) Xeon(R) CPU   E5530  @ 2.40GHz
Stepping:  5
CPU MHz:   2393.791
BogoMIPS:  4787.24
Virtualization:VT-x
L1d cache: 32K
L1i cache: 32K
L2 cache:  256K
L3 cache:  8192K
NUMA node0 CPU(s): 0,2,4,6
NUMA node1 CPU(s): 1,3,5,7

I appreciate that a lot is system-dependent and that I can't really help
you help me very much. It also should be noted that my multi runs are
multiple walker metadynamics run and are slowing down because there are
large bias potentials in memory that need to be communicated around too.
As I said I haven't had a chance to make separate benchmark runs but have
just made observations based upon existing runs.

Best wishes
James

> Performance tuning is highly dependent on the simulation system and
> the hardware you're running on. Questions like the ones you pose are
> impossible to answer meaningfully without *full* log files (and
> hardware specs including network).
>
> Have you checked the performance checklist I linked above?
> --
> Szilárd
>
>
> On Wed, Sep 21, 2016 at 11:36 AM,   wrote:
>> I wonder whether what I see that -np 108 and -ntomp 2 is best comes from
>> using -multi 6 with 8-CPU nodes. That level of parallelism may then be
>> necessary to trigger automatic segregation of PP and PME ranks. I'm not
>> sure if I tried -np 54 and -ntomp 4, which would probably also do it. I
>> compared mostly on 196 CPUs then found going up to 216 was better than
>> 196
>> with -ntomp 2 and pure MPI (-ntomp 1) was considerably worse for both.
>> Would people recommend to go back to 196 which allows 4 whole nodes per
>> replica and playing with -npme and -ntomp_pme?
>>
>>> Hi Thanh Le,
>>>
>>> Assuming all the nodes are the same (9 nodes with 12 CPUs) then you
>>> could
>>> try the following
>>>
>>> mpirun -np 9 --map-by node mdrun -ntomp 12 ...
>>> mpirun -np 18 mdrun -ntomp 6 ...
>>> mpirun -np 54 mdrun -ntomp 2 ...
>>>
>>> Which of these works best will depend on your setup.
>>>
>>> Using the whole cluster for one job may not be the most efficient way.
>>> I
>>> found on our cluster that once I reach 216 CPUs (equivalent settings
>>> from
>>> the queuing system to -np 108 and -ntomp 2), I can't do better by
>>> adding
>>> more nodes (where presumably communication becomes an issue). In
>>> addition
>>> to running -multi or -multidir jobs, which takes the load off
>>> communication a bit, it may also be worth having separate jobs and
>>> using
>>> -pin on and -pinoffset.
>>>
>>> Best wishes
>>> James
>>>
 Hi everyone,
 I have a question concerning running gromacs in parallel. I have read
 over
 the
 http://manual.gromacs.org/documentation/5.1/user-guide/mdrun-performance.html
 
 but I still dont quite understand how to run it efficiently.
 My gromacs version is 4.5.4
 The cluster I am using has CPUs total: 108 and 4 hosts up.
 The node iam using:
 Architecture:  x86_64
 CPU op-mode(s):32-bit, 64-bit
 Byte Order:Little Endian
 CPU(s):12
 On-line CPU(s) list:   0-11
 Thread(s) per core:2
 Core(s) per socket:6
 Socket(s): 1
 NUMA node(s):  1
 Vendor ID: AuthenticAMD
 CPU family:21
 Model: 2
 Stepping:  0
 CPU MHz:   1400.000
>

Re: [gmx-users] Running Gromacs in parallel

[jkrieger]

I wonder whether what I see that -np 108 and -ntomp 2 is best comes from
using -multi 6 with 8-CPU nodes. That level of parallelism may then be
necessary to trigger automatic segregation of PP and PME ranks. I'm not
sure if I tried -np 54 and -ntomp 4, which would probably also do it. I
compared mostly on 196 CPUs then found going up to 216 was better than 196
with -ntomp 2 and pure MPI (-ntomp 1) was considerably worse for both.
Would people recommend to go back to 196 which allows 4 whole nodes per
replica and playing with -npme and -ntomp_pme?

> Hi Thanh Le,
>
> Assuming all the nodes are the same (9 nodes with 12 CPUs) then you could
> try the following
>
> mpirun -np 9 --map-by node mdrun -ntomp 12 ...
> mpirun -np 18 mdrun -ntomp 6 ...
> mpirun -np 54 mdrun -ntomp 2 ...
>
> Which of these works best will depend on your setup.
>
> Using the whole cluster for one job may not be the most efficient way. I
> found on our cluster that once I reach 216 CPUs (equivalent settings from
> the queuing system to -np 108 and -ntomp 2), I can't do better by adding
> more nodes (where presumably communication becomes an issue). In addition
> to running -multi or -multidir jobs, which takes the load off
> communication a bit, it may also be worth having separate jobs and using
> -pin on and -pinoffset.
>
> Best wishes
> James
>
>> Hi everyone,
>> I have a question concerning running gromacs in parallel. I have read
>> over
>> the
>> http://manual.gromacs.org/documentation/5.1/user-guide/mdrun-performance.html
>> 
>> but I still dont quite understand how to run it efficiently.
>> My gromacs version is 4.5.4
>> The cluster I am using has CPUs total: 108 and 4 hosts up.
>> The node iam using:
>> Architecture:  x86_64
>> CPU op-mode(s):32-bit, 64-bit
>> Byte Order:Little Endian
>> CPU(s):12
>> On-line CPU(s) list:   0-11
>> Thread(s) per core:2
>> Core(s) per socket:6
>> Socket(s): 1
>> NUMA node(s):  1
>> Vendor ID: AuthenticAMD
>> CPU family:21
>> Model: 2
>> Stepping:  0
>> CPU MHz:   1400.000
>> BogoMIPS:  5200.57
>> Virtualization:AMD-V
>> L1d cache: 16K
>> L1i cache: 64K
>> L2 cache:  2048K
>> L3 cache:  6144K
>> NUMA node0 CPU(s): 0-11
>> MPI is already installed. I also have permission to use the cluster as
>> much as I can.
>> My question is: how should I write my mdrun command run to utilize all
>> the
>> possible cores and nodes?
>> Thanks,
>> Thanh Le
>> --
>> 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] Running Gromacs in parallel

[jkrieger]

Hi Thanh Le,

Assuming all the nodes are the same (9 nodes with 12 CPUs) then you could
try the following

mpirun -np 9 --map-by node mdrun -ntomp 12 ...
mpirun -np 18 mdrun -ntomp 6 ...
mpirun -np 54 mdrun -ntomp 2 ...

Which of these works best will depend on your setup.

Using the whole cluster for one job may not be the most efficient way. I
found on our cluster that once I reach 216 CPUs (equivalent settings from
the queuing system to -np 108 and -ntomp 2), I can't do better by adding
more nodes (where presumably communication becomes an issue). In addition
to running -multi or -multidir jobs, which takes the load off
communication a bit, it may also be worth having separate jobs and using
-pin on and -pinoffset.

Best wishes
James

> Hi everyone,
> I have a question concerning running gromacs in parallel. I have read over
> the
> http://manual.gromacs.org/documentation/5.1/user-guide/mdrun-performance.html
> 
> but I still dont quite understand how to run it efficiently.
> My gromacs version is 4.5.4
> The cluster I am using has CPUs total: 108 and 4 hosts up.
> The node iam using:
> Architecture:  x86_64
> CPU op-mode(s):32-bit, 64-bit
> Byte Order:Little Endian
> CPU(s):12
> On-line CPU(s) list:   0-11
> Thread(s) per core:2
> Core(s) per socket:6
> Socket(s): 1
> NUMA node(s):  1
> Vendor ID: AuthenticAMD
> CPU family:21
> Model: 2
> Stepping:  0
> CPU MHz:   1400.000
> BogoMIPS:  5200.57
> Virtualization:AMD-V
> L1d cache: 16K
> L1i cache: 64K
> L2 cache:  2048K
> L3 cache:  6144K
> NUMA node0 CPU(s): 0-11
> MPI is already installed. I also have permission to use the cluster as
> much as I can.
> My question is: how should I write my mdrun command run to utilize all the
> possible cores and nodes?
> Thanks,
> Thanh Le
> --
> 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
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>

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Re: [gmx-users] Martini Lipid Bilayer Simulation

[jkrieger]

Dear Prithvi,

This sounds like diffusion through the periodic boundaries to me and not a
problem at all. Try trjconv to fix it for visualisation as suggested at
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

Best wishes
James

> Dear gmx users,
>
> I am trying to perform Martini CG simulations containing peptide helices
> embedded into POPC bilayer with Gromacs 5.1.2. I have prepared the system
> using the insane.py script provided on the Martini website. I am running
> the system using the mdp file (martini_v2.x_new.mdp) obtained from Martini
> website. The entries of the mdp file are as follows -
> ;
> ; STANDARD MD INPUT OPTIONS FOR MARTINI 2.x
> ; Updated 15 Jul 2015 by DdJ
> ;
> ; for use with GROMACS 5
> ; For a thorough comparison of different mdp options in combination with
> the Martini force field, see:
> ; D.H. de Jong et al., Martini straight: boosting performance using a
> shorter cutoff and GPUs, submitted.
>
> title= Martini
>
> ; TIMESTEP IN MARTINI
> ; Most simulations are numerically stable with dt=40 fs,
> ; however better energy conservation is achieved using a
> ; 20-30 fs timestep.
> ; Time steps smaller than 20 fs are not required unless specifically
> stated
> in the itp file.
>
> integrator   = md
> dt   = 0.02
> nsteps   = 2
> nstcomm  = 100
> comm-grps = System
>
> nstxout  = 0
> nstvout  = 0
> nstfout  = 0
> nstlog   = 1
> nstenergy= 1000
> nstxout-compressed   = 1
> compressed-x-precision   = 100
> compressed-x-grps=
> energygrps   = Protein POPC W
>
> ; NEIGHBOURLIST and MARTINI
> ; To achieve faster simulations in combination with the
> Verlet-neighborlist
> ; scheme, Martini can be simulated with a straight cutoff. In order to
> ; do so, the cutoff distance is reduced 1.1 nm.
> ; Neighborlist length should be optimized depending on your hardware
> setup:
> ; updating ever 20 steps should be fine for classic systems, while
> updating
> ; every 30-40 steps might be better for GPU based systems.
> ; The Verlet neighborlist scheme will automatically choose a proper
> neighborlist
> ; length, based on a energy drift tolerance.
> ;
> ; Coulomb interactions can alternatively be treated using a
> reaction-field,
> ; giving slightly better properties.
> ; Please realize that electrostVatic interactions in the Martini model are
> ; not considered to be very accurate to begin with, especially as the
> ; screening in the system is set to be uniform across the system with
> ; a screening constant of 15. When using PME, please make sure your
> ; system properties are still reasonable.
> ;
> ; With the polarizable water model, the relative electrostatic screening
> ; (epsilon_r) should have a value of 2.5, representative of a
> low-dielectric
> ; apolar solvent. The polarizable water itself will perform the explicit
> screening
> ; in aqueous environment. In this case, the use of PME is more realistic.
>
>
> cutoff-scheme= Verlet
> nstlist  = 20
> ns_type  = grid
> pbc  = xyz
> verlet-buffer-tolerance  = 0.005
>
> coulombtype  = cutoff
> coulomb-modifier = Potential-shift-verlet
> rcoulomb = 1.1
> epsilon_r= 15; 2.5 (with polarizable water)
> vdw_type = cutoff
> vdw-modifier = Potential-shift-verlet
> rvdw = 1.1
>
> ; MARTINI and TEMPERATURE/PRESSURE
> ; normal temperature and pressure coupling schemes can be used.
> ; It is recommended to couple individual groups in your system separately.
> ; Good temperature control can be achieved with the velocity rescale
> (V-rescale)
> ; thermostat using a coupling constant of the order of 1 ps. Even better
> ; temperature control can be achieved by reducing the temperature coupling
> ; constant to 0.1 ps, although with such tight coupling (approaching
> ; the time step) one can no longer speak of a weak-coupling scheme.
> ; We therefore recommend a coupling time constant of at least 0.5 ps.
> ; The Berendsen thermostat is less suited since it does not give
> ; a well described thermodynamic ensemble.
> ;
> ; Pressure can be controlled with the Parrinello-Rahman barostat,
> ; with a coupling constant in the range 4-8 ps and typical compressibility
> ; in the order of 10e-4 - 10e-5 bar-1. Note that, for equilibration
> purposes,
> ; the Berendsen barostat probably gives better results, as the Parrinello-
> ; Rahman is prone to oscillating behaviour. For bilayer systems the
> pressure
> ; coupling should be done semiisotropic.
>
> tcoupl   = v-rescale
> tc-grps  = Protein POPC W
> tau_t= 1.0  1.0 1.0
> ref_t= 310 310 310
> Pcoupl   = parrinello-rahman
> Pcoupl

Re: [gmx-users] MPI GPU job failed

[jkrieger]

I'd suggest installing another gromacs version without MPI then. Your
system doesn't have enough CPU nodes to support it I imagine as you asked
for 2 and got 1. You could try the following first though:

mpirun -np 2 gmx_mpi mdrun -ntomp 10 -v -s 62.tpr -gpu_id 01

That way rather than having 1 mpi process with 20 openmp threads you have
2 mpi processes with 10 openmp threads if it works. I'm not sure whether
it will though.

> Hi, I used your suggested command line, but it failed with the following
> messages:
>
>
> ---
> Program gmx mdrun, VERSION 5.1.3
> Source code file:
> /home/albert/Downloads/gromacs/gromacs-5.1.3/src/gromacs/gmxlib/gmx_detect_hardware.cpp,
> line: 458
>
> Fatal error:
> Incorrect launch configuration: mismatching number of PP MPI processes
> and GPUs per node.
> gmx_mpi was started with 1 PP MPI process per node, but you provided 2
> GPUs.
> For more information and tips for troubleshooting, please check the
> GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> ---
>
> Halting program gmx mdrun
> --
> MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
> with errorcode 1.
>
> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
> You may or may not see output from other processes, depending on
> exactly when Open MPI kills them.
> --
> Using 1 MPI process
> Using 20 OpenMP threads
>
> 2 GPUs user-selected for this run.
> Mapping of GPU IDs to the 1 PP rank in this node: 0,1
>
>
> ---
> Program gmx mdrun, VERSION 5.1.3
> Source code file:
> /home/albert/Downloads/gromacs/gromacs-5.1.3/src/gromacs/gmxlib/gmx_detect_hardware.cpp,
> line: 458
>
> Fatal error:
> Incorrect launch configuration: mismatching number of PP MPI processes
> and GPUs per node.
> gmx_mpi was started with 1 PP MPI process per node, but you provided 2
> GPUs.
> For more information and tips for troubleshooting, please check the
> GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> ---
>
>
>
>
> On 08/11/2016 01:18 PM, jkrie...@mrc-lmb.cam.ac.uk wrote:
>> The problem is you compiled gromacs with mpi (hence the default _mpi in
>> your command). You therefore need to set the number of mpi processes
>> rather than threads. The appropriate command would instead be the
>> following:
>>
>> mpirun -np 2 gmx_mpi mdrun -v -s 62.tpr -gpu_id 01
>>
>> Alternatively you could compile a different gromacs version without mpi.
>> This should have thread-mpi and openmp by default if you leave out
>> DGMX_MPI=ON from the cmake command.
>>
>> Best wishes
>> James
>
> --
> Gromacs Users mailing list
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> * Please search the archive at
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Re: [gmx-users] MPI GPU job failed

[jkrieger]

The problem is you compiled gromacs with mpi (hence the default _mpi in
your command). You therefore need to set the number of mpi processes
rather than threads. The appropriate command would instead be the
following:

mpirun -np 2 gmx_mpi mdrun -v -s 62.tpr -gpu_id 01

Alternatively you could compile a different gromacs version without mpi.
This should have thread-mpi and openmp by default if you leave out
DGMX_MPI=ON from the cmake command.

Best wishes
James

> Hello:
>
> I try to run command:
>
>
> gmx_mpi mdrun -nt 2 -v -s 62.tpr -gpu_id 01
>
> but it failed with messages:
>
> ---
> Program gmx mdrun, VERSION 5.1.3
> Source code file:
> /home/albert/Downloads/gromacs/gromacs-5.1.3/src/programs/mdrun/resource-division.cpp,
> line: 625
>
> Fatal error:
> Setting the total number of threads is only supported with thread-MPI
> and GROMACS was compiled without thread-MPI
> For more information and tips for troubleshooting, please check the
> GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
> MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
> with errorcode 1.
> ---
>
>
>
> On 08/11/2016 06:50 AM, Nikhil Maroli wrote:
>> gmx mdrun -nt X -v -deffnm XXX -gpu_id XYZ
>>
>> What about this?
>>
>> Assign sufficient number of threads
>
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Re: [gmx-users] Plumed-2.1.0 Gromacs-5.0.2 installation error

[jkrieger]

The duplicate reference to Plumed.o problem reasserts itself when
compiling with GPU as the make install step re-runs cmake. The solution
here is to follow my previous protocol then after running the make install
step you delete the duplicate reference again and run the make install
step again. This is now with gromacs-5.0.4 and plumed-2.1.3 using default
compilers rather than specifying any.

>
>> On Thursday, June 11, 2015 at 4:30:41 PM UTC+1, James Krieger wrote:
>> I've found a work-around: using -pe openmpi #nodes with -l dedicated
#threads/node (24 in my case) and OMP_NUM_THREADS #threads/nodes.
>>
>>> On Wednesday, June 10, 2015 at 4:19:49 PM UTC+1, James Krieger wrote:
>>> Something's still not right. At this point GROMACS is MPI-aware and
can spread across multiple computers (nodes) when submitted to SGE
with -pe openmpi in the submission script. However when adding asking
it to use plumed for metad it fails unless it stays on a single
machine (specified with -pe smp). It's not a problem of plumed not
being compiled in MPI mode as using plumed to report on CVs without
metad works across multiple nodes.
>>>
>>> On Wednesday, June 10, 2015 at 1:38:19 PM UTC+1, James Krieger wrote:
>>> Actually that solution wasn't quite right because I didn't have the
mpi  compilers set up properly. That resulted in gromacs not being
mpi-aware but rather launching a separate mdrun_mpi process on each
node requested.
>>>
>>> Instead here's an updated solution that uses the default mpicc and
mpicxx wrappers (from openmpi-1.5.4 on my system).
>>>
>>> 1. configure/make/install plumed with addition of -fPIC to CFLAGS in
Makefile.conf before making (plumed-2.1.2 appears to need to be built
in the src directory)
>>>
>>> tar -xvzf plumed-2.1.2.tgz
>>> mv plumed-2.1.2 plumed-2.1.2-src
>>> mkdir plumed-2.1.2-install
>>> cd plumed-2.1.2-src
>>> ./configure --prefix=/lmb/home/jkrieger/
>>> bin/plumed-2.1.2-install/ CC=mpicc CXX=mpicxx
>>> manually add -fPIC to CFLAGS in Makefile.conf (done using vi)
>>> make VERBOSE=1 | & tee m.txt
>>> make install VERBOSE=1 | & tee mi.txt
>>> update PATH, LD_LIBRARY_PATH and PLUMED_KERNEL (added to ~/.login on
my system and applied by logging out and back in again)
>>>
>>> 2. patch plumed onto gromacs in --runtime mode (as per recommendation
of GB)
>>>
>>> cd ~/bin
>>> cp -r gromacs-5.0.4-src/ gromacs-5.0.4-src-plumed/
>>> mkdir gromacs-5.0.4-build-plumed
>>> mkdir gromacs-5.0.4-install-plumed
>>> cd gromacs-5.0.4-src-plumed/
>>> plumed patch -p --runtime
>>>
>>> 3. configure/make/install gromacs with separate src/build/install
directories (as per recommendation of MA) with removal of duplicate
reference to Plumed.o from
build-dir/src/gromacs/CMakeFiles/libgromacs.dir/link.txt (as per
recommendation of GB)
>>>
>>> cd ../gromacs-5.0.4-build-plumed
>>> cmake -DGMX_MPI=ON ../gromacs-5.0.4-src-plumed/
-DGMX_BUILD_OWN_FFTW=ON
-DCMAKE_INSTALL_PREFIX=/lmb/home/jkrieger/bin/gromacs-5.0.4-install-plumed
-DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpicxx
>>> remove duplicate reference to Plumed.o from
build-dir/src/gromacs/CMakeFiles/libgromacs.dir/link.txt (again with
vi)
>>> make VERBOSE=1 | & tee m.txt
>>> make install VERBOSE=1 | & tee mi.txt
>>> update PATH and LD_LIBRARY_PATH (vi ~/.login, log out, log in again)
>>>
>>>
>>> On Tuesday, June 9, 2015 at 7:23:14 PM UTC+1, James Krieger wrote:
>>> Here is the solution. Thanks to both Giovanni Bussi and Mark Abraham
for your help.
>>>
>>> 0. configure/make/install mpi compilers (separate src, build and
install directories are used as suggested by MA)
>>>
>>> tar -xvzfc mpich-3.1.4.tar.gz mpich-3.1.4-src
>>> mkdir mpich-3.1.4-build
>>> mkdir mpich-3.1.4-install
>>> cd mpich-3.1.4-build
>>> ../mpich-3.1.4-src/configure
--prefix=/lmb/home/jkrieger/bin/mpich-3.1.4-install | & tee c.txt
>>> make VERBOSE=1 | & tee m.txt
>>> make install VERBOSE=1 | & tee mi.txt
>>>
>>> 1. configure/make/install plumed with addition of -fPIC to CFLAGS in
Makefile.conf before making (plumed-2.1.2 appears to need to be built
in the src directory)
>>>
>>> tar -xvzfc plumed-2.1.2.tgz plumed-2.1.2-src
>>> mkdir plumed-2.1.2-install
>>> cd plumed-2.1.2-src
>>> ./configure --prefix=/lmb/home/jkrieger/bin/plumed-2.1.2-install/
CC=/lmb/home/jkrieger/bin/mpich-3.1.4-install/bin/mpicc
CXX=/lmb/home/jkrieger/bin/mpich-3.1.4-install/bin/mpicxx
>>> manually add -fPIC to

Re: [gmx-users] Plumed

[jkrieger]

Dear Alex,

There are a wide range of methods available in Plumed for free energy
calculation and enhanced sampling. I think the main benefit is the
collective variable based analyses such as metadynamics and umbrella
sampling. It also has ways of combining these with e.g. parallel tempering
and other replica exchange methods for further enhanced sampling. Whether
you need these methods or are happy with what's implemented in GROMACS
alone depends on what you want to do.

It's not too difficult to link them though. The one thing that's a bit
annoying for linking to GROMACS 5 is a duplicate reference to Plumed.o
from build-dir/src/gromacs/CMakeFiles/libgromacs.dir/link.txt, which you
have to remove. Here's my workflow for it, which works for patching Plumed
2.1.3 to GROMACS 5.0.4:
https://groups.google.com/forum/#!topic/plumed-users/stlK9-kaa6A

The step of adding to -fPIC to CFLAGS is no longer necessary as that was
fixed in Plumed 2.1.3 but otherwise you can follow the steps and it works.
You probably also want to set the suffixes in cmake with
-DGMX_DEFAULT_SUFFIX=OFF -DGMX_BINARY_SUFFIX=_mod -DGMX_LIBS_SUFFIX=_mod
changing mode to whatever you want to distinguish the plumed version from
another version. That said GROMACS with Plumed can perform GROMACS-only
runs absolutely fine so you could just make your Plumed version(s) your
dominant version(s).

Best wishes
James

> Dear Gromacs user,
>
> Before spending time on linking Gromacs to Plumed and learning it in order
> to do free energy calculations, I was wondering if Plumed does something
> extra more than our normal free energy calculation, FEP, or PMF in Gromacs
> or if it makes life easier in order to do these staff respect to the
> normal
> methods in Gromacs? In another word what is the necessity for it, if there
> is any?
>
> Thanks,
> Regards,
> Alex
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
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Re: [gmx-users] electrostatic energy calculation

[jkrieger]

The advantage is you can set new .tpr settings such as energygrps based
upon what you see in simulation. A rerun is for analysis and you can do it
many times as you think of new things to look at.

While we're on this topic, can anyone comment on how reproducible and
trustworthy a rerun is compared to say PBSA or GBSA?

Thanks
James

> Thank you Mark.
>
> On Tuesday, August 2, 2016, Mark Abraham  wrote:
>
>> Hi,
>>
>> Rerun is exactly that. You present some frames from a previous run (or
>> any
>> old frames) and mdrun says what the energies and forces are for those
>> configurations. Maybe with a different .tpr with different settings.
>> Your
>> call - but you are not "doing a run" any more. No configurations are
>> updated from forces, etc.
>>
>> Mark
>>
>> On Tue, Aug 2, 2016 at 7:37 PM Maryam Kowsar > >
>> wrote:
>>
>> > Thank you all. What James suggested seems to work. I just wonder what
>> the
>> > benefit of rerun option is. If I start the run from the begining with
>> a
>> > change in .mdp it leads to the same results I suppose.
>> > Thanks.
>> >
>> > On Tuesday, August 2, 2016, Mark Abraham > 
>> > > ');>>
>> wrote:
>> >
>> > > Yes, as I said.
>> > >
>> > > Mark
>> > >
>> > > On Tue, 2 Aug 2016 15:31 >
>> wrote:
>> > >
>> > > > Thanks Justin and Mark. Yes that could be it. I thought I had
>> tried
>> > both
>> > > > two and more energygrps with and without GPU and that two had
>> worked
>> on
>> > > > both but I can only find logs with more than two energygrps for
>> the
>> > jobs
>> > > > with GPU. I can't see any kind of warning. I am using GROMACS
>> 5.0.4 -
>> > do
>> > > > you mean a newer version than that would bring this up better?
>> > > >
>> > > > Best wishes
>> > > > James
>> > > >
>> > > > > Hi,
>> > > > >
>> > > > > Rerun works with any number of energy groups, but probably what
>> > you've
>> > > > > done
>> > > > > is run one of your reruns on a GPU, which doesn't support energy
>> > > groups,
>> > > > > and missed the warning mdrun issues. Recent versions are more
>> helpful
>> > > at
>> > > > > bringing this to your attention.
>> > > > >
>> > > > > Mark
>> > > > >
>> > > > > On Tue, Aug 2, 2016 at 1:54 PM > > wrote:
>> > > > >
>> > > > >> That's interesting Alex. mdrun -rerun only works with two
>> energygrps
>> > > (I
>> > > > >> put more then all g_energy terms come to zero) but you're
>> saying
>> > > normal
>> > > > >> mdrun works with any number. I don't know if that's intentional
>> or
>> > > > >> whether
>> > > > >> the developers would like me to make a Redmine..
>> > > > >>
>> > > > >> > Hi there,
>> > > > >> >
>> > > > >> > g_energy or gmx energy just lists the short-ranged non-bonded
>> > > > >> potential
>> > > > >> > energies of those species which have been already indicated
>> in
>> > *.mdp
>> > > > >> file
>> > > > >> > by "energygrps", like energygrps   = A B C, then g_energy
>> would
>> > > offer
>> > > > >> you
>> > > > >> > something like  Coul-SR: A-B , LJ-SR: B-C and so on.
>> > > > >> >
>> > > > >> > Cheers,
>> > > > >> > Alex
>> > > > >> >
>> > > > >> > On Tue, Aug 2, 2016 at 11:26 AM, Maryam Kowsar
>> > > > >> >
>> > > > >> > wrote:
>> > > > >> >
>> > > > >> >> Dear all,
>> > > > >> >>
>> > > > >> >> I want to calculate the electrostatic energy (coulomb SR and
>> LR)
>> > > for
>> > > > >> a
>> > > > >> >> set
>> > > > >> >> of molecules during the whole simulation. I used g_energy -f
>> > > ener.edr
>> > > > >> -o
>> > > > >> >> (with or without -nmol option), but it only gives me 1
>> average
>> > > output
>> > > > >> >> for
>> > > > >> >> the last step.I tried g_enemat -f -etot (-emat) but it stops
>> > > needing
>> > > > >> a
>> > > > >> >> group.dat file. Is there a way to calculate coulomb energy
>> in
>> all
>> > > > >> steps
>> > > > >> >> preferably for a set of desired charged molecules?
>> > > > >> >> 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!
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>> http://www.gromacs.org/Support/Mailing_Lists
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>> > > > >> >
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>> > > or
>> > > > >> send
>> > > > >> > a mail to gmx-users-requ...@gromacs.org .
>> > > > >> >
>> > > > >>
>> > > 

Re: [gmx-users] electrostatic energy calculation

[jkrieger]

Thanks Justin and Mark. Yes that could be it. I thought I had tried both
two and more energygrps with and without GPU and that two had worked on
both but I can only find logs with more than two energygrps for the jobs
with GPU. I can't see any kind of warning. I am using GROMACS 5.0.4 - do
you mean a newer version than that would bring this up better?

Best wishes
James

> Hi,
>
> Rerun works with any number of energy groups, but probably what you've
> done
> is run one of your reruns on a GPU, which doesn't support energy groups,
> and missed the warning mdrun issues. Recent versions are more helpful at
> bringing this to your attention.
>
> Mark
>
> On Tue, Aug 2, 2016 at 1:54 PM  wrote:
>
>> That's interesting Alex. mdrun -rerun only works with two energygrps (I
>> put more then all g_energy terms come to zero) but you're saying normal
>> mdrun works with any number. I don't know if that's intentional or
>> whether
>> the developers would like me to make a Redmine..
>>
>> > Hi there,
>> >
>> > g_energy or gmx energy just lists the short-ranged non-bonded
>> potential
>> > energies of those species which have been already indicated in *.mdp
>> file
>> > by "energygrps", like energygrps   = A B C, then g_energy would offer
>> you
>> > something like  Coul-SR: A-B , LJ-SR: B-C and so on.
>> >
>> > Cheers,
>> > Alex
>> >
>> > On Tue, Aug 2, 2016 at 11:26 AM, Maryam Kowsar
>> 
>> > wrote:
>> >
>> >> Dear all,
>> >>
>> >> I want to calculate the electrostatic energy (coulomb SR and LR) for
>> a
>> >> set
>> >> of molecules during the whole simulation. I used g_energy -f ener.edr
>> -o
>> >> (with or without -nmol option), but it only gives me 1 average output
>> >> for
>> >> the last step.I tried g_enemat -f -etot (-emat) but it stops needing
>> a
>> >> group.dat file. Is there a way to calculate coulomb energy in all
>> steps
>> >> preferably for a set of desired charged molecules?
>> >> 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.
>> >
>>
>>
>> --
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>>
>> * Please search the archive at
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>> posting!
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>>
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Re: [gmx-users] electrostatic energy calculation

[jkrieger]

That's interesting Alex. mdrun -rerun only works with two energygrps (I
put more then all g_energy terms come to zero) but you're saying normal
mdrun works with any number. I don't know if that's intentional or whether
the developers would like me to make a Redmine..

> Hi there,
>
> g_energy or gmx energy just lists the short-ranged non-bonded potential
> energies of those species which have been already indicated in *.mdp file
> by "energygrps", like energygrps   = A B C, then g_energy would offer you
> something like  Coul-SR: A-B , LJ-SR: B-C and so on.
>
> Cheers,
> Alex
>
> On Tue, Aug 2, 2016 at 11:26 AM, Maryam Kowsar 
> wrote:
>
>> Dear all,
>>
>> I want to calculate the electrostatic energy (coulomb SR and LR) for a
>> set
>> of molecules during the whole simulation. I used g_energy -f ener.edr -o
>> (with or without -nmol option), but it only gives me 1 average output
>> for
>> the last step.I tried g_enemat -f -etot (-emat) but it stops needing a
>> group.dat file. Is there a way to calculate coulomb energy in all steps
>> preferably for a set of desired charged molecules?
>> 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.
>>
> --
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> * Please search the archive at
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> posting!
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Re: [gmx-users] electrostatic energy calculation

[jkrieger]

Yes you need to use mdrun with the -rerun option. I did this as follows:

1. use make_ndx to add the desired selections into your index
2. make a new mdp with the energygrps option listing two index items by name
3. grompp -f rerun.mdp -c npt.gro -p topol.top -o rerun.tpr -n index.ndx
4. mdrun -v -deffnm rerun -rerun md.trr
5. gmx energy -f rerun.edr and select the terms corresponding to coulomb
SR and LR

You can use the -sum option of g_energy to sum these terms together.

Best wishes
James

> Dear all,
>
> I want to calculate the electrostatic energy (coulomb SR and LR) for a set
> of molecules during the whole simulation. I used g_energy -f ener.edr -o
> (with or without -nmol option), but it only gives me 1 average output for
> the last step.I tried g_enemat -f -etot (-emat) but it stops needing a
> group.dat file. Is there a way to calculate coulomb energy in all steps
> preferably for a set of desired charged molecules?
> 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
>
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> a mail to gmx-users-requ...@gromacs.org.
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Re: [gmx-users] protein and ligand is not forming complex after completing simulation

[jkrieger]

Yes, you should probably do multiple steps of trjconv. Do the pbc
correction first and then dump the final frame from the resulting
trajectory if it's the final frame you want. You could also do that with
the -b flag and enter the final time.

> So you mean to say that simulation is correct. But the problem is after
> that?
>
> On Wed, Jul 27, 2016 at 5:51 PM, Justin Lemkul  wrote:
>
>>
>>
>> On 7/27/16 8:18 AM, Swagata Patra wrote:
>>
>>> For trjconv i used the following command:
>>>
>>> trjconv_d -s md_0_1.tpr -f md_0_1.xtc -n index.ndx -o trj.pdb -pbc mol
>>> -ur
>>> compact -dt 3
>>>
>>>
>> The PBC fitting routines sometimes struggle with large -dt.  You're
>> basically just trying to dump out the final frame, which is redundant
>> with
>> what you're doing below.  If you want to obtain a PBC-corrected
>> trajectory,
>> follow the link I provided.
>>
>> For editconf I simply used : editconf_d -f md_0_1.gro -o md_0_1.pdb
>>>
>>> I have analyzed the H-bonds between protein and ligand, there showing
>>> formation of H-bonds.
>>>
>>> if ligand is dissociating, what could be the reason?
>>>
>>>
>> Bad topology, incorrect run settings, etc.  But from the simple matter
>> of
>> disagreement above, I doubt there's actually a problem.  Nearly always,
>> "dissociation" is just a PBC issue that needs to be handled carefully.
>>
>> -Justin
>>
>>
>>
>>> On Wed, Jul 27, 2016 at 5:40 PM,  wrote:
>>>
>>> Hi Swagata,

 Perhaps your ligand is dissociating during the simulation. What frames
 are
 you looking at with trjconv and editconf? If these are different you
 may
 be seeing bound and unbound snapshots.

 Best wishes
 James

 hi everyone,
>
> I  simulated protein-ligand complex for 30ns and then visualize the
> complex
> after simulation in pymol.
>
> I got the .pdb file using two commands from final simulated file.
> One is using trjconv, from .xtc to .pdb. When I am visualizing this
> .pdb
> file, protein and ligand has not formed any complex.
> Another one is using editconf, from .gro to .pdb. When I am
> visualizing
> this .pdb file, protein and ligand  formed  complex.
>
> Why is this happening? Can anyone explain it?
>
> Thanks in advance.
>
> --
> Swagata Patra
> M.Tech (Biotech)
> JRF
> IIT Guwahati
> --
> Gromacs Users mailing list
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>>>
>>>
>>>
>> --
>> ==
>>
>> 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
>>
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>>
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Re: [gmx-users] protein and ligand is not forming complex after completing simulation

[jkrieger]

Your editconf command presumably looks at the final frame of the
simulation, which were stored into the .gro at the end of the run.

Your trjconv command would give you a set of frames in the pdb, which
you'd see in pymol as states. Why did you pick 3? I'd pick a smaller
number and look at more frames. You could also do this with -skip rather
than -dt so you don't have to think in picoseconds.

If you have h-bonds throughout the simulation then they aren't
dissociating. It was just something to think about as complexes aren't
stable in real life so there's a chance they could dissociate in
simulations too. This chance is of course quite small unless you have a
very high k-off that comes into the same timescale as MD.

> For trjconv i used the following command:
>
> trjconv_d -s md_0_1.tpr -f md_0_1.xtc -n index.ndx -o trj.pdb -pbc mol -ur
> compact -dt 3
>
> For editconf I simply used : editconf_d -f md_0_1.gro -o md_0_1.pdb
>
> I have analyzed the H-bonds between protein and ligand, there showing
> formation of H-bonds.
>
> if ligand is dissociating, what could be the reason?
>
>
> On Wed, Jul 27, 2016 at 5:40 PM,  wrote:
>
>> Hi Swagata,
>>
>> Perhaps your ligand is dissociating during the simulation. What frames
>> are
>> you looking at with trjconv and editconf? If these are different you may
>> be seeing bound and unbound snapshots.
>>
>> Best wishes
>> James
>>
>> > hi everyone,
>> >
>> > I  simulated protein-ligand complex for 30ns and then visualize the
>> > complex
>> > after simulation in pymol.
>> >
>> > I got the .pdb file using two commands from final simulated file.
>> > One is using trjconv, from .xtc to .pdb. When I am visualizing this
>> .pdb
>> > file, protein and ligand has not formed any complex.
>> > Another one is using editconf, from .gro to .pdb. When I am
>> visualizing
>> > this .pdb file, protein and ligand  formed  complex.
>> >
>> > Why is this happening? Can anyone explain it?
>> >
>> > Thanks in advance.
>> >
>> > --
>> > Swagata Patra
>> > M.Tech (Biotech)
>> > JRF
>> > IIT Guwahati
>> > --
>> > Gromacs Users mailing list
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Re: [gmx-users] protein and ligand is not forming complex after completing simulation

[jkrieger]

Hi Swagata,

Perhaps your ligand is dissociating during the simulation. What frames are
you looking at with trjconv and editconf? If these are different you may
be seeing bound and unbound snapshots.

Best wishes
James

> hi everyone,
>
> I  simulated protein-ligand complex for 30ns and then visualize the
> complex
> after simulation in pymol.
>
> I got the .pdb file using two commands from final simulated file.
> One is using trjconv, from .xtc to .pdb. When I am visualizing this .pdb
> file, protein and ligand has not formed any complex.
> Another one is using editconf, from .gro to .pdb. When I am visualizing
> this .pdb file, protein and ligand  formed  complex.
>
> Why is this happening? Can anyone explain it?
>
> Thanks in advance.
>
> --
> Swagata Patra
> M.Tech (Biotech)
> JRF
> IIT Guwahati
> --
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Re: [gmx-users] minor edits to a .gro file

[jkrieger]

Plumed has a dumpatoms command (see
http://plumed.github.io/doc-v2.1/user-doc/html/_d_u_m_p_a_t_o_m_s.html ).
You can create virtual atoms whose position is defined based on existing
atoms or groups thereof. Plumed can be used as a stand-alone driver or
patched onto gromacs for on-the-fly analysis and biasing.

Best wishes
James

> Hi all,
>
> I¹m looking to open a .gro file, add in six hydrogen dummy atoms (I can
> rename the atom name/type, I just need the correct x, y and z coords) to
> the end of an amino acid sidechain and save whilst preserving as much of
> the .gro format as it can.
>
>
> I would normally load the crystal/derived structure as a .pdb into
> Avogadro or smaller fragments from Gaussian output. Unfortunately, as I
> have defined a completely bespoke post-translation amino acid I can¹t
> restore to .pdb with the aim of using Avogadro, too much can go wrong.
>
>
> Recommendations for Gromacs friendly editing tools would be appreciated.
>
> Thanks
> Anthony
>
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Re: [gmx-users] PCA problems

[jkrieger]

ok thanks Tsjerk. I think that makes sense now.

Best wishes
James

> Hi James,
>
> That's silly! Ambiguous means that the same structure can have multiple
> solutions in a fit. The fit to a single reference structure (with more
> than
> three atoms) is never ambiguous. Can never, by definition!
>
> Now if you have two reference structures at hand, and they have (quite)
> different structures, then fitting on one may give a different ensemble
> from fitting on the other. The fit is not consistent, and the
> inconsistency
> is worse for flexible molecules. Different ensembles will mean different
> correlations, thus giving different principal components.
>
> Progressive fitting does not solve the problem. In fact, progressive
> fitting _is_ ambiguous. Let's say we have a series of conformations ABCAC.
> Then we  fit C once to B, which was fitted to A, and later we have C
> fitted
> to A, which was fitted to the previous C. Note that in practice the
> situation will be much worse as we can approach a certain configuration
> from many sides. Using B as reference will yield a fit that is different
> from using A as reference, so the structure C will have two different
> orientations in the resulting ensemble. Hence, the fit is ambiguous.
>
> For structured proteins, the difference will not matter much. However, in
> long trajectories there may be an added contribution (drift) of the
> orientation.
>
> Hope it helps,
>
> Tsjerk
>
> On Wed, Jun 8, 2016 at 5:33 PM,  wrote:
>
>> Thanks Tsjerk,
>>
>> Isn't the progressive fit supposed to rotate everything back into the
>> same
>> orientation without having to worry about inferring that orientation
>> from
>> a reference structure that doesn't align well? Each configuration should
>> in theory align well to its predecessor all the way back to the starting
>> structure (which is what I'd usually take as a reference anyway).
>>
>> The original note I was thinking of says as follows:
>>
>> '''Before a PCA, all structures should be superimposed onto a common
>> reference
>> structure. This can be problematic for very flexible systems such as
>> peptides,
>> where the fit may be ambiguous, leading to artificial structural
>> transitions. In
>> certain cases, such problems may be alleviated by using a progressive
>> fit,
>> where
>> each structure is superimposed onto the previous one. It is also
>> important
>> to note
>> that when results of different PCAs are to be compared with each other,
>> then
>> each individual PCA should be based on the same reference structure used
>> for
>> superposition.'''
>>
>> Please could you explain further what it is I have misunderstood.
>>
>> Also would you say a progressive fit is a bad idea for more structured
>> proteins?
>>
>> Many thanks
>> James
>>
>> > Hi James,
>> >
>> > 'Spurious alignment' is the dependence of the resulting ensemble on
>> the
>> > reference structure. Unfortunately, that's not solved by a progressive
>> > fit.
>> > Rather, in a progressive fit, the same configuration can have multiple
>> > orientations, based on the previous structures, which is also
>> problematic
>> > when you're trying to understand spatial correlations between atoms
>> within
>> > their reference frame.
>> >
>> > Cheers,
>> >
>> > Tsjerk
>> >
>> > On Wed, Jun 8, 2016 at 9:27 AM,  wrote:
>> >
>> >> Dear Teresa,
>> >>
>> >> That sounds like a periodic boundary issue to me. It could be fixed
>> by
>> >> using a tpr instead of a gro as the gmx covar manual says "All
>> >> structures
>> >> are fitted to the structure in the structure file. When this is not a
>> >> run
>> >> input file periodicity will not be taken into account." Alternatively
>> if
>> >> you don't have a tpr you could use gmx trjconv first with -pbc whole
>> or
>> >> -pbc nojump.
>> >>
>> >> I also remember reading (I think it was in the Hayward and de Groot
>> >> review
>> >> 2008) that fitting peptides to a reference structure can cause
>> spurious
>> >> alignments. I don't know if this is also related to what you're
>> seeing
>> >> but
>> >> it might be worth using gmx trjconv again with-fit progressive then
>> use
>> >> -nofit in gmx covar.
>> >>
>> >> Best wishes
>> >> James
>> >>
>> >> > Dear GROMACS community
>> >> >
>> >> > I am trying to complete a PCA analysis of my peptide adsorbed to a
>> >> > surface. However when I use :
>> >> >
>> >> > gmx covar -s trajectory.gro  -f md_golp_vacuo.xtc
>> >> >
>> >> > and select the protein for both the least squares fit and
>> covariance
>> >> > calculation, followed by
>> >> >
>> >> >
>> >> > gmx anaeig -s trajectory.gro -f md_golp_vacuo.trr -filt filter1.gro
>> >> > -first 1 -last 1 -skip 100
>> >> >
>> >> > and I select the peptide for the least squares and covariance
>> >> > calculation
>> >> >
>> >> > My peptide is now broken up into pieces. Is this right?
>> >> >
>> >> >
>> >> >
>> >> > Best
>> >> > Teresa
>> >> > --
>> >> > Gromacs Users mailing list
>> >> >
>> >> > * Please search the archive at
>> >> > http://www.groma

Re: [gmx-users] PCA problems

[jkrieger]

Thanks Tsjerk,

Isn't the progressive fit supposed to rotate everything back into the same
orientation without having to worry about inferring that orientation from
a reference structure that doesn't align well? Each configuration should
in theory align well to its predecessor all the way back to the starting
structure (which is what I'd usually take as a reference anyway).

The original note I was thinking of says as follows:

'''Before a PCA, all structures should be superimposed onto a common
reference
structure. This can be problematic for very flexible systems such as
peptides,
where the fit may be ambiguous, leading to artificial structural
transitions. In
certain cases, such problems may be alleviated by using a progressive fit,
where
each structure is superimposed onto the previous one. It is also important
to note
that when results of different PCAs are to be compared with each other, then
each individual PCA should be based on the same reference structure used for
superposition.'''

Please could you explain further what it is I have misunderstood.

Also would you say a progressive fit is a bad idea for more structured
proteins?

Many thanks
James

> Hi James,
>
> 'Spurious alignment' is the dependence of the resulting ensemble on the
> reference structure. Unfortunately, that's not solved by a progressive
> fit.
> Rather, in a progressive fit, the same configuration can have multiple
> orientations, based on the previous structures, which is also problematic
> when you're trying to understand spatial correlations between atoms within
> their reference frame.
>
> Cheers,
>
> Tsjerk
>
> On Wed, Jun 8, 2016 at 9:27 AM,  wrote:
>
>> Dear Teresa,
>>
>> That sounds like a periodic boundary issue to me. It could be fixed by
>> using a tpr instead of a gro as the gmx covar manual says "All
>> structures
>> are fitted to the structure in the structure file. When this is not a
>> run
>> input file periodicity will not be taken into account." Alternatively if
>> you don't have a tpr you could use gmx trjconv first with -pbc whole or
>> -pbc nojump.
>>
>> I also remember reading (I think it was in the Hayward and de Groot
>> review
>> 2008) that fitting peptides to a reference structure can cause spurious
>> alignments. I don't know if this is also related to what you're seeing
>> but
>> it might be worth using gmx trjconv again with-fit progressive then use
>> -nofit in gmx covar.
>>
>> Best wishes
>> James
>>
>> > Dear GROMACS community
>> >
>> > I am trying to complete a PCA analysis of my peptide adsorbed to a
>> > surface. However when I use :
>> >
>> > gmx covar -s trajectory.gro  -f md_golp_vacuo.xtc
>> >
>> > and select the protein for both the least squares fit and covariance
>> > calculation, followed by
>> >
>> >
>> > gmx anaeig -s trajectory.gro -f md_golp_vacuo.trr -filt filter1.gro
>> > -first 1 -last 1 -skip 100
>> >
>> > and I select the peptide for the least squares and covariance
>> > calculation
>> >
>> > My peptide is now broken up into pieces. Is this right?
>> >
>> >
>> >
>> > Best
>> > Teresa
>> > --
>> > Gromacs Users mailing list
>> >
>> > * Please search the archive at
>> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> > posting!
>> >
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>> >
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>> > 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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>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
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Re: [gmx-users] PCA problems

[jkrieger]

Dear Teresa,

That sounds like a periodic boundary issue to me. It could be fixed by
using a tpr instead of a gro as the gmx covar manual says "All structures
are fitted to the structure in the structure file. When this is not a run
input file periodicity will not be taken into account." Alternatively if
you don't have a tpr you could use gmx trjconv first with -pbc whole or
-pbc nojump.

I also remember reading (I think it was in the Hayward and de Groot review
2008) that fitting peptides to a reference structure can cause spurious
alignments. I don't know if this is also related to what you're seeing but
it might be worth using gmx trjconv again with-fit progressive then use
-nofit in gmx covar.

Best wishes
James

> Dear GROMACS community
>
> I am trying to complete a PCA analysis of my peptide adsorbed to a
> surface. However when I use :
>
> gmx covar -s trajectory.gro  -f md_golp_vacuo.xtc
>
> and select the protein for both the least squares fit and covariance
> calculation, followed by
>
>
> gmx anaeig -s trajectory.gro -f md_golp_vacuo.trr -filt filter1.gro
> -first 1 -last 1 -skip 100
>
> and I select the peptide for the least squares and covariance
> calculation
>
> My peptide is now broken up into pieces. Is this right?
>
>
>
> Best
> Teresa
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
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Re: [gmx-users] Simulating a protein dimer

[jkrieger]

I solved the problem by using an em.tpr with pbc nojump for my dimers. pbc
whole takes the monomers as whole units and does as you described. pbc
nojump starting from md.tpr like I'd normally do didn't work because
partial boundary crossings had happened before the production md.

> I encountered similar problem after simulating a pentameric model of
> protein. It was solved by applying pbc whole in gmx trjconv.
>
> Sent from my iPhone
>
>> On 07-Jun-2016, at 7:49 pm, Biplab Ghosh  wrote:
>>
>> Dear Gromacs Users,
>>
>> I am trying to simulate a protein dimer using Gromacs-5.1.2. Gromacs
>> completed successfully
>> but when analysing the trajectories, the monomers are flying apart and
>> coming back again!
>>
>> I used the following Gromacs commands/options:
>>
>> gmx trjconv -s protein-md.tpr -f protein-md.xtc  -pbc mol -center -ur
>> compact -o protein-md-center.xtc
>>
>> gmx trjconv -s protein-md.tpr -f  protein-md-center.xtc -fit rot+trans
>> -o
>> protein-md-center-fit.xtc
>>
>> gmx trjconv -s protein-processed.gro -f protein-md-center-fit.xtc -o
>> protein-movie.pdb -tu ns -dt 1
>>
>>
>> I would really appreciate any help on this.
>>
>> Regards,
>> Biplab.
>>
>> --
>> "Simplicity in life allows you to focus on what's important"
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Re: [gmx-users] allosteric effect

[jkrieger]

Hi,

I wouldn't expect to be able to distinguish MWC from KNF in 200 ns but I
imagine this could reveal at least part of the underlying communication
mechanism. I'm also trying to use MD for this and would be interested in
people's views.

Best wishes
James

> Hi Qasim,
>
> Do you assume MWC or KNF like allostery, and conformational based,
> dynamics
> based or mixed?
>
> Cheers,
>
> Tsjerk
>
> On Fri, Jun 3, 2016 at 2:54 AM, Qasim Pars  wrote:
>
>> Dear gmx users,
>>
>> The protein I have simulated over 200 ns with GROMACS is dimer and shows
>> positive allostery. Based on experimental data, the second ligand of
>> protein has greater binding affinity than the first ligand. I would like
>> to
>> prove the positive allosteric effect of protein by some analyses. But I
>> really don't know which analyses helps me to investigate/look into the
>> allosteric effect. Could you please suggest me some useful analyses to
>> investigate the allosteric effect (except for RMSD, RMSF)? I have
>> simulations for singly liganded, doubly liganded and apo state.
>>
>> Thanks a lot, in advance.
>> --
>> Qasim Pars
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
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>
>
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Re: [gmx-users] grompp_d and mdrun_d in gromacs 5.1.2

[jkrieger]

Hi Emma,

You should be able to compile gromacs 5.1.2 with double precision and then
use gmx_d grompp and gmx_d mdrun. I think the symbolic link should include
the _d so the grompp_d and mdrun_d commands should still work too.

Best wishes
James

> Hi,
> i wonder if there is a command for running with double precision in
> VERSION 5.1.2, like grompp_d in VERSION 4.6.5?
>
> Best regards,
> Emma
> ---
> Emma Ahlstrand
> PhD student
>
> Linnaeus University
> Faculty of Health and Life Sciences
> 391 82 Kalmar / 351 95 Växjö
> Sweden
>
> +46 772 28 80 00 Telephone exchange
> +46 480 44 61 52 Direct
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> emma.ahlstr...@lnu.se
> http://lnu.se/ccbg
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>
> Challenging educations. Prominent research. Linnaeus University – a
> modern, international university in Småland, Sweden.
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Re: [gmx-users] Analysis

[jkrieger]

Hi,

If you can't save a GROMACS compatible xtc from vmd then I suggest using
the mdconvert tool from mdtraj. It can convert between most commonly used
md trajectory formats and have used it for both CHARMM dcd to
GROMACS-compatible xtc and GROMACS xtc to a dcd that is readable by ProDy
with no problems.

Best wishes
James

> Hi,
>
> How to analyze in gromacs 4.5.7 from the  dcd file? I have vmd installed
> in my computer.
>
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Re: [gmx-users] Restart simulation from checkpoint file with fewer nodes

[jkrieger]

ok thanks

> Hi,
>
> Yes, that's one way to work around the problem. In some places, a module
> subsystem can be used to take care of the selection automatically, but you
> don't want to set one up for just you to use.
>
> Mark
>
> On Sun, May 15, 2016 at 11:48 AM  wrote:
>
>> Thanks Mark,
>>
>> My sysadmins have let me install my own GROMACS versions and have not
>> informed me of any such mechanism. Would you suggest I qrsh into a node
>> of
>> each type and build an mdrun-only version on each? I'd then select a
>> particular node type for a submit script with the relevant mdrun.
>>
>> Many thanks
>> James
>>
>> > Hi,
>> >
>> > On Sat, May 14, 2016 at 1:09 PM  wrote:
>> >
>> >> In case it's relevant/interesting to anyone, here are the details on
>> our
>> >> cluster nodes:
>> >>
>> >> nodes   #   model   # cores cpu
>> >> model
>> >>   RAM   node_type
>> >> fmb01 - fmb33   33  IBM HS21XM  8   3 GHz
>> >> Xeon
>> >> E5450
>> >>  16GB   hs21
>> >> fmb34 - fmb42   9   IBM HS228   2.4
>> GHz
>> >> Xeon E5530
>> >> 16GBhs22
>> >> fmb43 - fmb88   45  Dell PE M6108   2.4
>> GHz
>> >> Xeon E5530
>> >>  16GB   m610
>> >> fmb88 - fmb90   3   Dell PE M610+   12  3.4
>> GHz
>> >> Xeon X5690
>> >>   48GB  m610+
>> >> fmb91 - fmb202  112 Dell PE M62024 (HT) 2.9
>> GHz
>> >> Xeon E5-2667
>> >>64GB m620
>> >> fmb203 - fmb279 77  Dell PE M62024 (HT) 3.5
>> GHz
>> >> Xeon E5-2643 v2 64GB
>> >> m620+
>> >> fmb280 - fmb359 80  Dell PE M63024 (HT) 3.4
>> GHz
>> >> Xeon E5-2643 v3 64GB
>> >> m630
>> >>
>> >> I could only run GROMACS 4.6.2 on the last three node types and I
>> >> believe
>> >> the same is true for 5.0.4
>> >>
>> >
>> > Sure. GROMACS is designed to target whichever hardware was selected at
>> > configure time, which your sysadmins for such a heterogeneous cluster
>> > should have documented somewhere. They should also be making available
>> to
>> > you a mechanism to target your jobs to nodes where they can run
>> programs
>> > that use the hardware efficiently, or providing GROMACS installations
>> that
>> > work regardless of which node you are actually on. You might like to
>> > respectfully remind them of the things we say at
>> >
>> http://manual.gromacs.org/documentation/5.1.2/install-guide/index.html#portability-aspects
>> > (These thoughts are common to earlier versions also.)
>> >
>> > Mark
>> >
>> >
>> > Best wishes
>> >> James
>> >>
>> >> > I have found that only some kinds of nodes on our cluster work for
>> >> gromacs
>> >> > 4.6 (the ones we call m620, m620+ and m630 but not others - I can
>> >> check
>> >> > the details tomorrow). I haven't tested it again now I'm using 5.0
>> so
>> >> > don't know if that's still an issue but if it is it could explain
>> why
>> >> your
>> >> > restart failed even and the initial run didn't.
>> >> >
>> >> >> thanks a lot for your fast response.
>> >> >>
>> >> >> I have tried it, and it failed. I ask in this forum just to make
>> >> sure.
>> >> >> However, there was something in my cluster that probably make it
>> >> failed.
>> >> >> I'll handle it first and then retry to restart again.
>> >> >>
>> >> >> Regards,
>> >> >>
>> >> >> Husen
>> >> >>
>> >> >> On Sat, May 14, 2016 at 7:58 AM, Justin Lemkul 
>> >> wrote:
>> >> >>
>> >> >>>
>> >> >>>
>> >> >>> On 5/13/16 8:53 PM, Husen R wrote:
>> >> >>>
>> >>  Dear all
>> >> 
>> >>  Does simulation able to be restarted from checkpoint file with
>> >> fewer
>> >>  nodes ?
>> >>  let's say, at the first time, I run simulation with 3 nodes. At
>> >>  running
>> >>  time, one of those nodes is crashed and the simulation is
>> >> terminated.
>> >> 
>> >>  I want to restart that simulation immadiately based on
>> checkpoint
>> >> file
>> >>  with
>> >>  the remaining 2 nodes. does gromacs support such case ?
>> >>  I need help.
>> >> 
>> >> >>>
>> >> >>> Have you tried it?  It should work.  You will probably get a note
>> >> about
>> >> >>> the continuation not being exact due to a change in the number of
>> >> >>> cores,
>> >> >>> but the run should proceed fine.
>> >> >>>
>> >> >>> -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
>> >> >>>
>> >> >>> ==
>> >> >>> 

Re: [gmx-users] Restart simulation from checkpoint file with fewer nodes

[jkrieger]

Thanks Mark,

My sysadmins have let me install my own GROMACS versions and have not
informed me of any such mechanism. Would you suggest I qrsh into a node of
each type and build an mdrun-only version on each? I'd then select a
particular node type for a submit script with the relevant mdrun.

Many thanks
James

> Hi,
>
> On Sat, May 14, 2016 at 1:09 PM  wrote:
>
>> In case it's relevant/interesting to anyone, here are the details on our
>> cluster nodes:
>>
>> nodes   #   model   # cores cpu
>> model
>>   RAM   node_type
>> fmb01 - fmb33   33  IBM HS21XM  8   3 GHz
>> Xeon
>> E5450
>>  16GB   hs21
>> fmb34 - fmb42   9   IBM HS228   2.4 GHz
>> Xeon E5530
>> 16GBhs22
>> fmb43 - fmb88   45  Dell PE M6108   2.4 GHz
>> Xeon E5530
>>  16GB   m610
>> fmb88 - fmb90   3   Dell PE M610+   12  3.4 GHz
>> Xeon X5690
>>   48GB  m610+
>> fmb91 - fmb202  112 Dell PE M62024 (HT) 2.9 GHz
>> Xeon E5-2667
>>64GB m620
>> fmb203 - fmb279 77  Dell PE M62024 (HT) 3.5 GHz
>> Xeon E5-2643 v2 64GB
>> m620+
>> fmb280 - fmb359 80  Dell PE M63024 (HT) 3.4 GHz
>> Xeon E5-2643 v3 64GB
>> m630
>>
>> I could only run GROMACS 4.6.2 on the last three node types and I
>> believe
>> the same is true for 5.0.4
>>
>
> Sure. GROMACS is designed to target whichever hardware was selected at
> configure time, which your sysadmins for such a heterogeneous cluster
> should have documented somewhere. They should also be making available to
> you a mechanism to target your jobs to nodes where they can run programs
> that use the hardware efficiently, or providing GROMACS installations that
> work regardless of which node you are actually on. You might like to
> respectfully remind them of the things we say at
> http://manual.gromacs.org/documentation/5.1.2/install-guide/index.html#portability-aspects
> (These thoughts are common to earlier versions also.)
>
> Mark
>
>
> Best wishes
>> James
>>
>> > I have found that only some kinds of nodes on our cluster work for
>> gromacs
>> > 4.6 (the ones we call m620, m620+ and m630 but not others - I can
>> check
>> > the details tomorrow). I haven't tested it again now I'm using 5.0 so
>> > don't know if that's still an issue but if it is it could explain why
>> your
>> > restart failed even and the initial run didn't.
>> >
>> >> thanks a lot for your fast response.
>> >>
>> >> I have tried it, and it failed. I ask in this forum just to make
>> sure.
>> >> However, there was something in my cluster that probably make it
>> failed.
>> >> I'll handle it first and then retry to restart again.
>> >>
>> >> Regards,
>> >>
>> >> Husen
>> >>
>> >> On Sat, May 14, 2016 at 7:58 AM, Justin Lemkul 
>> wrote:
>> >>
>> >>>
>> >>>
>> >>> On 5/13/16 8:53 PM, Husen R wrote:
>> >>>
>>  Dear all
>> 
>>  Does simulation able to be restarted from checkpoint file with
>> fewer
>>  nodes ?
>>  let's say, at the first time, I run simulation with 3 nodes. At
>>  running
>>  time, one of those nodes is crashed and the simulation is
>> terminated.
>> 
>>  I want to restart that simulation immadiately based on checkpoint
>> file
>>  with
>>  the remaining 2 nodes. does gromacs support such case ?
>>  I need help.
>> 
>> >>>
>> >>> Have you tried it?  It should work.  You will probably get a note
>> about
>> >>> the continuation not being exact due to a change in the number of
>> >>> cores,
>> >>> but the run should proceed fine.
>> >>>
>> >>> -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!
>> >>
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>> >>
>> >> * For (un)subscribe re

Re: [gmx-users] Restart simulation from checkpoint file with fewer nodes

[jkrieger]

In case it's relevant/interesting to anyone, here are the details on our
cluster nodes:

nodes   #   model   # cores cpu model   
 
  RAM   node_type
fmb01 - fmb33   33  IBM HS21XM  8   3 GHz Xeon 
E5450  
 16GB   hs21
fmb34 - fmb42   9   IBM HS228   2.4 GHz Xeon 
E5530 
16GBhs22
fmb43 - fmb88   45  Dell PE M6108   2.4 GHz Xeon 
E5530
 16GB   m610
fmb88 - fmb90   3   Dell PE M610+   12  3.4 GHz Xeon 
X5690   
  48GB  m610+
fmb91 - fmb202  112 Dell PE M62024 (HT) 2.9 GHz Xeon 
E5-2667
   64GB m620
fmb203 - fmb279 77  Dell PE M62024 (HT) 3.5 GHz Xeon 
E5-2643 v2 64GB
m620+
fmb280 - fmb359 80  Dell PE M63024 (HT) 3.4 GHz Xeon 
E5-2643 v3 64GB
m630

I could only run GROMACS 4.6.2 on the last three node types and I believe
the same is true for 5.0.4

Best wishes
James

> I have found that only some kinds of nodes on our cluster work for gromacs
> 4.6 (the ones we call m620, m620+ and m630 but not others - I can check
> the details tomorrow). I haven't tested it again now I'm using 5.0 so
> don't know if that's still an issue but if it is it could explain why your
> restart failed even and the initial run didn't.
>
>> thanks a lot for your fast response.
>>
>> I have tried it, and it failed. I ask in this forum just to make sure.
>> However, there was something in my cluster that probably make it failed.
>> I'll handle it first and then retry to restart again.
>>
>> Regards,
>>
>> Husen
>>
>> On Sat, May 14, 2016 at 7:58 AM, Justin Lemkul  wrote:
>>
>>>
>>>
>>> On 5/13/16 8:53 PM, Husen R wrote:
>>>
 Dear all

 Does simulation able to be restarted from checkpoint file with fewer
 nodes ?
 let's say, at the first time, I run simulation with 3 nodes. At
 running
 time, one of those nodes is crashed and the simulation is terminated.

 I want to restart that simulation immadiately based on checkpoint file
 with
 the remaining 2 nodes. does gromacs support such case ?
 I need help.

>>>
>>> Have you tried it?  It should work.  You will probably get a note about
>>> the continuation not being exact due to a change in the number of
>>> cores,
>>> but the run should proceed fine.
>>>
>>> -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.
>>>
>> --
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Re: [gmx-users] Restart simulation from checkpoint file with fewer nodes

[jkrieger]

I have found that only some kinds of nodes on our cluster work for gromacs
4.6 (the ones we call m620, m620+ and m630 but not others - I can check
the details tomorrow). I haven't tested it again now I'm using 5.0 so
don't know if that's still an issue but if it is it could explain why your
restart failed even and the initial run didn't.

> thanks a lot for your fast response.
>
> I have tried it, and it failed. I ask in this forum just to make sure.
> However, there was something in my cluster that probably make it failed.
> I'll handle it first and then retry to restart again.
>
> Regards,
>
> Husen
>
> On Sat, May 14, 2016 at 7:58 AM, Justin Lemkul  wrote:
>
>>
>>
>> On 5/13/16 8:53 PM, Husen R wrote:
>>
>>> Dear all
>>>
>>> Does simulation able to be restarted from checkpoint file with fewer
>>> nodes ?
>>> let's say, at the first time, I run simulation with 3 nodes. At running
>>> time, one of those nodes is crashed and the simulation is terminated.
>>>
>>> I want to restart that simulation immadiately based on checkpoint file
>>> with
>>> the remaining 2 nodes. does gromacs support such case ?
>>> I need help.
>>>
>>
>> Have you tried it?  It should work.  You will probably get a note about
>> the continuation not being exact due to a change in the number of cores,
>> but the run should proceed fine.
>>
>> -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
>>
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>> 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] gromacs.org_gmx-users Digest, Vol 145, Issue 12

[jkrieger]

To convert this you need to remember that the square on the nm, which
should then be applied to the 10 A, making 100 A^2:
1000 kJ/(mol nm^2) = 1000 kJ/(mol (10 A)^2)) = 1000 kJ/(mol 100 A^2) =
1000/100 kJ/(mol A^2) = 10 kJ/(mol A^2)

Best wishes
James

> thanks Justin Lemkul.
> i am using all units in Angstrom and kj/mole. soif the default of disre-fc
> is 1000 kj mol-1 nm-2 , what it would be in kj mol-1 A-2. i am trying to
> convert it through google but the number isn't looking satisfying. i know
> 1nm =10 A.
>  Sana Saeed Khan,
> Research Assistant
> Chemoinformatics Lab
> Graduate Student, MS bioinfo
> Department of Bioinformatics
> Soongsil University, Seoul, South Korea.
>
>
>
> On Thursday, May 5, 2016 11:31 AM, Sana Saeed
>  wrote:
>
>
>
> Sana Saeed Khan,
> Research Assistant
> Chemoinformatics Lab
> Graduate Student, MS bioinfo
> Department of Bioinformatics
> Soongsil University, Seoul, South Korea.
>
>
>
>
> On Wednesday, May 4, 2016 9:33 PM,
> "gromacs.org_gmx-users-requ...@maillist.sys.kth.se"
>  wrote:
> Send gromacs.org_gmx-users mailing list submissions to
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>
> Today's Topics:
>
>1. Re: restraints definition in mdp (Justin Lemkul)
>2. persistent jumps in trajectories (morpheus)
>3. Re: restraints definition in mdp (Justin Lemkul)
>4. Re: persistent jumps in trajectories (Justin Lemkul)
>5. restarts (ingram)
>
>
> --
>
> Message: 1
> Date: Wed, 4 May 2016 06:04:01 -0400
> From: Justin Lemkul 
> To: gmx-us...@gromacs.org, Sana Saeed 
> Subject: Re: [gmx-users] restraints definition in mdp
> Message-ID: 
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
>
> On 5/4/16 4:08 AM, Sana Saeed wrote:
>> hi gromacs experts
>> i have applied distance, angle and dihedral restraints to my ligand in a
>> protein's pocket so that it doesnt roam around when i turn off all
>> interactions during simulation. do i need to mention about these
>> restraints in the mdp file? i am using gromacs 5.0 and 5.1. i have used
>> intermolecular_interactions directive for defining these restraints.
>
> There is nothing in the .mdp file related to these.
>
>> MY SECOND QUESTION is that the force constant i used is 41.840 kj/mol/K
>> for angle and dihedral restr. does that mean that the Force constant for
>> distance restraint is also 41.840? as i am calculating free energy of
>> restraints (part of absolute binding F.E) so i need force constant for
>> distance also.
>>
>
> The force constant can be whatever you want it to be.
>
> -Justin
>
>> [ intermolecular-interactions ]
>> [ distance_restraints ]
>> ;   i j type label  funct loup1up2
>> weight
>>   768  2131 1 0  1   0.640512   0.8405121.84051
>> 1
>>
>> [ angle_restraints ]
>> ;   aiajakal  typethA  fcAmultA  thB  fcB
>> multB
>>770   7682131  768  1  43.4200.0   1  43.420   41.840
>>1
>>768   2131   2125  2131 1 114.890.0   1  114.89   41.840
>>   1
>>
>> [ dihedral_restraints ]
>> ;   aiajakal  typephiA dphiA  fcAphiB  dphiB
>>  fcB
>>   782  770   768   2131  1   -152.840  0.0  0.0-152.8400.0
>> 41.840
>>   770  768   2131  2125  1   -46.638  0.0  0.0 -46.638 0.0
>> 41.840
>>   768  2131  2125  2132  1   -42.465   0.0  0.0-42.465 0.0
>> 41.840
>>
>>
>> Sana Saeed Khan,
>> Research Assistant
>> Chemoinformatics Lab
>> Graduate Student, MS bioinfo
>> Department of Bioinformatics
>> Soongsil University, Seoul, South Korea.
>>
>
> --
> ==
>
> 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
>
> ==
>
>
> --
>
> Message: 2
> Date: Wed, 4 May 2016 11:12:38 +0100
> From: morpheus 
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: [gmx-users] persistent jumps in trajectories
> Message-ID:
> 
> Content-Type: text/plain; charset=UTF-8
>
> Hi,
>
> I'm having problems getting jumps out of my trajectories. Usually I follow
> the suggestion of the G

Re: [gmx-users] MARTINI simulation of protein-protein recognition

[jkrieger]

ok shouldn't martinize do the equivalent to pdb2gmx, i.e. make the final
pdb or gro file and a corresponding topology? Your problem is with genbox
with thinks MEMBRANEsystem.gro is the solvent and therefore will not be
connected like protein and membrane. My suggestion to take the placements
from genbox but remake the pdb can presumably still be done to make input
for martinize just like it could for pdb2gmx.

Best wishes
James

> no pdb2gmx will not work because I am working with the martini CG models
>
> how I fix the issue it reorent the atom names by hands (coppy protein
> and lipids from the initial pdbs which were submitted to genbox to the
> complex.gro because initially I had properly oriented complexes).
>
> BTW where I can find smth useful regarding mdp options for the system
> which include 2 unbound protein comlexes. E.g how it better to define
> coupling groups for the barostat and thermostat assuming that 1
> proteis is inserted within the membrane and another is within the
> water.
>
> Thanks!!!
>
> J.
>
> 2016-04-19 15:54 GMT+02:00  :
>> How about aligning the original MEMBRANEsystem.gro and waterSOLprot.gro
>> onto the relevant part of solvatedNEW.gro in pymol (after converting to
>> PDB) and then creating and saving a new object from both parts which you
>> use as input for pdb2gmx to create the topology. That way both parts
>> have
>> their original residue orders.
>>
>>> a now I understand that genbox has reorented the order the residues in
>>> the protein which was embedded in the membrane used as the solvent >)
>>>
>>> is it possible to prevent the order of all residues in the system
>>> provided by -cs flag?
>>>
>>> 2016-04-19 15:14 GMT+02:00 James Starlight :
 btw I have tried to insert second molecular using just genbox having
 both components oriented properly in the space before

 g_genbox -cp waterSOLprot.gro -cs MEMBRANEsystem.gro -vdwd 0.21 -o
 solvatedNEW.gro -box 18 18 28

 than checking VMD solvatedNEW.gro - everything was looks perfect- the
 waterSOLprot has been placed in proper position and overlapped CG
 water has been removed.

 now running gromppt I received

 WARNING 1 [file system.top, line 49]:
   2886 non-matching atom names
   atom names from system.top will be used
   atom names from system.gro will be ignored


 I also should specify that after genbox I edited new topology.top
 manually
 putting chains of the proteins in correct order (like in new gro file
 produced by genbox) and putting correct number of W

 assuming that initially I have multi chain protein in the POPC
 membrane
 and using genbox I added to the system one new chain Z

 before
 [quote]Protein_A  1
 Protein_B  1
 Protein_C  1
 Protein_D  1
 Protein_E  1
 Protein_F  1
 Protein_G  1
 Protein_H  1
 Protein_I  1
 Protein_J  1
 Protein_K  1
 Protein_L  1
 Protein_M  1
 POPC   451
 CHOL 0
 POPC   451
 CHOL 0
 W61226
 NA+678
 CL-671[/quote]

 after
 [quote]Protein_Z  1
 Protein_A  1
 Protein_B  1
 Protein_C  1
 Protein_D  1
 Protein_E  1
 Protein_F  1
 Protein_G  1
 Protein_H  1
 Protein_I  1
 Protein_J  1
 Protein_K  1
 Protein_L  1
 Protein_M  1
 POPC   451
 CHOL 0
 POPC   451
 CHOL 0
 W60817
 NA+678
 CL-671[/quote]

 where I did mistake? Does genbox reorent atom order in the -cp
 waterSOLprot.gro -cs MEMBRANEsystem.gro ? Could it be fixed?

 2016-04-18 16:21 GMT+02:00 James Starlight :
> Ok thanks I will look into the tutorial!
>
> J.
>
> 2016-04-18 16:02 GMT+02:00 Kroon, P.C. :
>> @Michael: Yes, you are right, a protein is a protein. IIRC the
>> martinize
>> script does the same as pdb2gmx in this case.
>> @James: It really sounds like you want to do DAFT.
>> http://www.biotechnik.nat.uni-erlangen.de/research/boeckmann/downloads/DAFT/index.shtml
>> seems to contain an tutorial. Otherwise, consider contacting the
>> author of
>> the paper (T Wassenaar).
>>
>> Peter
>>
>> On Mon, Apr 18, 2016 at 3:51 PM, Smith, Micholas D.
>> 
>> wrote:
>>
>>> Hi James,
>>>
>>> My guess is that running a two (unbound) protein simulation with
>>> the
>>> MARTINI force-field will be the same as if it was all atom. Build
>>> two
>>> separate protein topologies (with Martini force-fields) as *.itp
>>> files to
>>> include in your *.top and go from there. The topology file is what
>>> grompp
>>> uses to determine bonding, so if the topology file

Re: [gmx-users] MARTINI simulation of protein-protein recognition

[jkrieger]

How about aligning the original MEMBRANEsystem.gro and waterSOLprot.gro
onto the relevant part of solvatedNEW.gro in pymol (after converting to
PDB) and then creating and saving a new object from both parts which you
use as input for pdb2gmx to create the topology. That way both parts have
their original residue orders.

> a now I understand that genbox has reorented the order the residues in
> the protein which was embedded in the membrane used as the solvent >)
>
> is it possible to prevent the order of all residues in the system
> provided by -cs flag?
>
> 2016-04-19 15:14 GMT+02:00 James Starlight :
>> btw I have tried to insert second molecular using just genbox having
>> both components oriented properly in the space before
>>
>> g_genbox -cp waterSOLprot.gro -cs MEMBRANEsystem.gro -vdwd 0.21 -o
>> solvatedNEW.gro -box 18 18 28
>>
>> than checking VMD solvatedNEW.gro - everything was looks perfect- the
>> waterSOLprot has been placed in proper position and overlapped CG
>> water has been removed.
>>
>> now running gromppt I received
>>
>> WARNING 1 [file system.top, line 49]:
>>   2886 non-matching atom names
>>   atom names from system.top will be used
>>   atom names from system.gro will be ignored
>>
>>
>> I also should specify that after genbox I edited new topology.top
>> manually
>> putting chains of the proteins in correct order (like in new gro file
>> produced by genbox) and putting correct number of W
>>
>> assuming that initially I have multi chain protein in the POPC membrane
>> and using genbox I added to the system one new chain Z
>>
>> before
>> [quote]Protein_A  1
>> Protein_B  1
>> Protein_C  1
>> Protein_D  1
>> Protein_E  1
>> Protein_F  1
>> Protein_G  1
>> Protein_H  1
>> Protein_I  1
>> Protein_J  1
>> Protein_K  1
>> Protein_L  1
>> Protein_M  1
>> POPC   451
>> CHOL 0
>> POPC   451
>> CHOL 0
>> W61226
>> NA+678
>> CL-671[/quote]
>>
>> after
>> [quote]Protein_Z  1
>> Protein_A  1
>> Protein_B  1
>> Protein_C  1
>> Protein_D  1
>> Protein_E  1
>> Protein_F  1
>> Protein_G  1
>> Protein_H  1
>> Protein_I  1
>> Protein_J  1
>> Protein_K  1
>> Protein_L  1
>> Protein_M  1
>> POPC   451
>> CHOL 0
>> POPC   451
>> CHOL 0
>> W60817
>> NA+678
>> CL-671[/quote]
>>
>> where I did mistake? Does genbox reorent atom order in the -cp
>> waterSOLprot.gro -cs MEMBRANEsystem.gro ? Could it be fixed?
>>
>> 2016-04-18 16:21 GMT+02:00 James Starlight :
>>> Ok thanks I will look into the tutorial!
>>>
>>> J.
>>>
>>> 2016-04-18 16:02 GMT+02:00 Kroon, P.C. :
 @Michael: Yes, you are right, a protein is a protein. IIRC the
 martinize
 script does the same as pdb2gmx in this case.
 @James: It really sounds like you want to do DAFT.
 http://www.biotechnik.nat.uni-erlangen.de/research/boeckmann/downloads/DAFT/index.shtml
 seems to contain an tutorial. Otherwise, consider contacting the
 author of
 the paper (T Wassenaar).

 Peter

 On Mon, Apr 18, 2016 at 3:51 PM, Smith, Micholas D. 
 wrote:

> Hi James,
>
> My guess is that running a two (unbound) protein simulation with the
> MARTINI force-field will be the same as if it was all atom. Build two
> separate protein topologies (with Martini force-fields) as *.itp
> files to
> include in your *.top and go from there. The topology file is what
> grompp
> uses to determine bonding, so if the topology file doesn't have the
> two
> proteins bound, they won't be. If I remember correctly, you can see
> an
> example (all-atom) topology file to work with if you use pdb2gmx for
> a pdb
> that contains 2 chains (with the proper flag the chains will be
> split).
>
> -Micholas
>
> ===
> Micholas Dean Smith, PhD.
> Post-doctoral Research Associate
> University of Tennessee/Oak Ridge National Laboratory
> Center for Molecular Biophysics
>
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of James
> Starlight 
> Sent: Monday, April 18, 2016 9:43 AM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] MARTINI simulation of protein-protein
> recognition
>
> It seems like smth very complicated :)
>
> I just need to put two different proteins in the system - one in the
> membrane (A) and one in the water (B) and simulate it independently
> 10
> times to collect statistics about associations of A and B during
> those
> runs. The problems that I don't know how to put 2 different unbound
> proteins in the MARTINI system.
>
> James
>
> 2016-0

Re: [gmx-users] You are applying a switch function to vdw forces or potentials from 0 to 1.2 nm

[jkrieger]

The problem is you have not set rvdw-switch and the default value is 0.
You should instead set this to something closer to rvdw such as 1.0

It looks like vdw-modifier: potential shift would be a better choice and
then rdw-switch isn't used.
See
http://manual.gromacs.org/documentation/5.1.1/user-guide/mdp-options.html#van-der-waals
for more details

Best wishes
James

>
> Hello: i'm running the grompp of NVT but during the run i have the
> following:NOTE: You are applying a switch function to vdw forces or
> potentials from 0 to 1.2 nm, which is more than half the interaction
> ranges whereas switch functions are intended to act only close to the
> cut-offWhat does it means? it' ¶ anything wrong?My rlist, rcoulomb and
> rvdw are 1.2 (in nm), vdwtype: cut-off, vdwmodifier: force-switch,
> coulombtype: PME. Should i decrease rlist, rcoulomb and rvdw? increase my
> rlist to 1.4? or change my vdwtype to switch?
> Thanks
> --
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Re: [gmx-users] Warning: you have generated 17732 solvent molecules which are not multiple of 11 .

[jkrieger]

You need to use a tool outside GROMACS to model in missing residues.
Discovery studio has capabilities to do this using MODELLER so you could
do that if you're comfortable with that software already (see
http://accelrys.com/services/training/life-science/protein-homology-modeling.html
which I just found through a Google search). I'm not sure what the issue
with the multiple of 11 is though.

Best wishes
James

> actually i m not getting how to proceed futher i m beginner to GROMACS
> it would be helpful if you can elaborate the process
>
> On 17 March 2016 at 21:54, Pradip Kaur  wrote:
>
>> so should i go for sol molecules :1612
>>  Na :11
>>
>> On 17 March 2016 at 21:44, Peter Stern 
>> wrote:
>>
>>> Missing atoms in GLU 474 is because the coordinates for the GLU side
>>> chain weren't resolved in the crystallographic data and aren't included
>>> in
>>> the pdb file.  Long bonds are probably because of missing residues.
>>> Check
>>> the pdb file for MISSING residues and atoms (listed in the header
>>> records).  Also, you can't just delete a residue and let Gromacs think
>>> that
>>> the preceding and following residues are connected (by an unphysical
>>> "long"
>>> bond).  The same goes for missing residues in the pdb file.
>>>
>>> I hope that the net charge was -5.999 otherwise, why add Na ions.  And
>>> as
>>> far as I know, 11*1612=17732.
>>>
>>> Peter Stern
>>>
>>> Sent from my iPad
>>>
>>> On 17 במרץ 2016, at 11:08, Pradip Kaur
>>> >> kaur.pradip...@gmail.com>> wrote:
>>>
>>> i am currently working with 2bbo.pdb protein ,i have edited this
>>> protein
>>> in
>>> Discovery studio 4.5 and deleted phenylalanine at 508 position , now i
>>> m
>>> running molecular dynamics simulation  in GROMACS 5.0.2 bt after
>>> running
>>> pdb2gmx  with  GROMOS96 53a6 force field Water model :spc216 ,it is
>>> showing
>>>
>>> Warning: Long Bond (161-163 = 1.78456 nm)
>>>
>>> Warning: Long Bond (840-842 = 0.357037 nm)
>>>
>>> Warning: Long Bond (2237-2239 = 0.636287 nm)
>>>
>>>
>>>
>>> WARNING: atom CG is missing in residue GLU 474 in the pdb file
>>>
>>>
>>>
>>>
>>>
>>> WARNING: atom CD is missing in residue GLU 474 in the pdb file
>>>
>>>
>>>
>>>
>>>
>>> WARNING: atom OE1 is missing in residue GLU 474 in the pdb file
>>>
>>>
>>>
>>>
>>>
>>> WARNING: atom OE2 is missing in residue GLU 474 in the pdb file
>>>
>>>
>>>
>>>
>>>
>>> ---
>>>
>>> Program pdb2gmx, VERSION 5.0.2
>>>
>>> Source code file:
>>> /build/buildd/gromacs-5.0.2/src/gromacs/gmxpreprocess/pdb2top.cpp,
>>> line:
>>> 1587
>>>
>>>
>>>
>>> Fatal error:
>>>
>>> There were 4 missing atoms in molecule Protein_chain_A, if you want to
>>> use
>>> this incomplete topology anyhow, use the option -missing
>>>
>>> For more information and tips for troubleshooting, please check the
>>> GROMACS
>>>
>>> website at http://www.gromacs.org/Documentation/Errors
>>>
>>>
>>> *But  after ignoring missing atoms ,when i am running grompp command it
>>> shows that the system has non zero integral charge of 5.999.*
>>>
>>> *i have added command genion to neutalise the charge by adding 6 Na
>>> ions
>>> .After running the command it says that you have generated 17732
>>> solvent
>>> molecules which are not multiple of 11 .*
>>>
>>> *can any one help me with this problem*
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>> posting!
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>>> send a mail to gmx-users-requ...@gromacs.org>> gmx-users-requ...@gromacs.org>.
>>> --
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>>
>>
>>
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Re: [gmx-users] Warning: you have generated 17732 solvent molecules which are not multiple of 11 .

[jkrieger]

Definitely use modeller first. Then go through everything again.

I'm happy you solved the problem with the multiple of 11. Perhaps Justin
or Mark or someone could comment on why it said that. While it makes sense
to replace solvent atoms with ions in most cases, I would have thought any
replacement would work including parts of proteins and ligands.

Best wishes
James

> Thank you for all your suggestion ,ya I did some mistake after adding Na
> ions   I selected system option (0)
> As per your suggestion when I selected Sol (13) my problem solved ...Do I
> need to go for modeller now or should I continue with this ...
> On 18-Mar-2016 12:41 pm,  wrote:
>
>> I'd suggest creating models with and without residue 508 in the target
>> sequence. MODELLER should be able to rebuild the loop without residue
>> 508
>> and then you won't have long bonds. A hole in a protein is not
>> physically
>> or biologically meaningful. Rather a deletion mutation will end up in
>> the
>> ribosome inserting the next amino acid and linking it by a normal
>> peptide
>> bond.
>>
>> You'd then have to set up the system again from the model and I agree
>> with
>> Peter that you should check what you're doing against a tutorial to
>> avoid
>> the solvent error.
>>
>> Best wishes
>> James
>>
>> > My project is on cystic fibrosis 508 del mutation ,what I m trying to
>> do
>> > is
>> > that I have taken nuclear binding domain with 508phenylalanine
>> (2bbo.pdb)
>> > and I deleted that 508 phenylalanine to create a similar situation as
>> what
>> > occurs in body in case of cystic fibrosis ...after minimization of
>> this
>> > protein I ll dock the protein with a corrector ...and will see the
>> binding
>> > energy
>> > On 18-Mar-2016 6:06 am, "Peter Stern" 
>> wrote:
>> >
>> >> As James said, if you are using Discovery Studio it can model missing
>> >> atoms and residues.  But why are you deleting a residue?  What do you
>> >> hope
>> >> to learn from this?  And don't just ignore missing atoms.
>> >>
>> >> I also don't understand the genion error, but I don't think you
>> reported
>> >> it exactly.  Didn't genion ask you to choose a solvent group and did
>> you
>> >> do
>> >> that correctly?  I certainly didn't mean that you should choose 1612
>> sol
>> >> molecules and 11 Na.  I simply meant that I didn't understand the
>> error
>> >> message since 17732 is divisible by 11.  I suspect that you didn't
>> >> choose
>> >> the correct group for solvent.
>> >>
>> >> Since you are a beginner may I suggest that you use one of the many
>> >> Gromacs tutorials available choosing one appropriate to what you are
>> >> trying
>> >> to do?  I am sure that you can find these easily enough with Google.
>> >>
>> >> Best regards?
>> >> Peter
>> >>
>> >> Sent from my iPhone
>> >>
>> >> > On 17 Mar 2016, at 12:27 PM, Pradip Kaur 
>> >> wrote:
>> >> >
>> >> > actually i m not getting how to proceed futher i m beginner to
>> GROMACS
>> >> > it would be helpful if you can elaborate the process
>> >> >
>> >> >> On 17 March 2016 at 21:54, Pradip Kaur 
>> >> wrote:
>> >> >>
>> >> >> so should i go for sol molecules :1612
>> >> >> Na :11
>> >> >>
>> >> >>> On 17 March 2016 at 21:44, Peter Stern
>> 
>> >> wrote:
>> >> >>>
>> >> >>> Missing atoms in GLU 474 is because the coordinates for the GLU
>> side
>> >> >>> chain weren't resolved in the crystallographic data and aren't
>> >> included in
>> >> >>> the pdb file.  Long bonds are probably because of missing
>> residues.
>> >> Check
>> >> >>> the pdb file for MISSING residues and atoms (listed in the header
>> >> >>> records).  Also, you can't just delete a residue and let Gromacs
>> >> think
>> >> that
>> >> >>> the preceding and following residues are connected (by an
>> unphysical
>> >> "long"
>> >> >>> bond).  The same goes for missing residues in the pdb file.
>> >> >>>
>> >> >>> I hope that the net charge was -5.999 otherwise, why add Na ions.
>> >> And
>> >> as
>> >> >>> far as I know, 11*1612=17732.
>> >> >>>
>> >> >>> Peter Stern
>> >> >>>
>> >> >>> Sent from my iPad
>> >> >>>
>> >> >>> On 17 במרץ 2016, at 11:08, Pradip Kaur
>> > >> > >> >>> kaur.pradip...@gmail.com>> wrote:
>> >> >>>
>> >> >>> i am currently working with 2bbo.pdb protein ,i have edited this
>> >> protein
>> >> >>> in
>> >> >>> Discovery studio 4.5 and deleted phenylalanine at 508 position ,
>> now
>> >> i
>> >> m
>> >> >>> running molecular dynamics simulation  in GROMACS 5.0.2 bt after
>> >> running
>> >> >>> pdb2gmx  with  GROMOS96 53a6 force field Water model :spc216 ,it
>> is
>> >> >>> showing
>> >> >>>
>> >> >>> Warning: Long Bond (161-163 = 1.78456 nm)
>> >> >>>
>> >> >>> Warning: Long Bond (840-842 = 0.357037 nm)
>> >> >>>
>> >> >>> Warning: Long Bond (2237-2239 = 0.636287 nm)
>> >> >>>
>> >> >>>
>> >> >>>
>> >> >>> WARNING: atom CG is missing in residue GLU 474 in the pdb file
>> >> >>>
>> >> >>>
>> >> >>>
>> >> >>>
>> >> >>>
>> >> >>> WARNING: atom CD is missing in residue GLU 474 in the pdb file

Re: [gmx-users] Warning: you have generated 17732 solvent molecules which are not multiple of 11 .

[jkrieger]

I'd suggest creating models with and without residue 508 in the target
sequence. MODELLER should be able to rebuild the loop without residue 508
and then you won't have long bonds. A hole in a protein is not physically
or biologically meaningful. Rather a deletion mutation will end up in the
ribosome inserting the next amino acid and linking it by a normal peptide
bond.

You'd then have to set up the system again from the model and I agree with
Peter that you should check what you're doing against a tutorial to avoid
the solvent error.

Best wishes
James

> My project is on cystic fibrosis 508 del mutation ,what I m trying to do
> is
> that I have taken nuclear binding domain with 508phenylalanine (2bbo.pdb)
> and I deleted that 508 phenylalanine to create a similar situation as what
> occurs in body in case of cystic fibrosis ...after minimization of this
> protein I ll dock the protein with a corrector ...and will see the binding
> energy
> On 18-Mar-2016 6:06 am, "Peter Stern"  wrote:
>
>> As James said, if you are using Discovery Studio it can model missing
>> atoms and residues.  But why are you deleting a residue?  What do you
>> hope
>> to learn from this?  And don't just ignore missing atoms.
>>
>> I also don't understand the genion error, but I don't think you reported
>> it exactly.  Didn't genion ask you to choose a solvent group and did you
>> do
>> that correctly?  I certainly didn't mean that you should choose 1612 sol
>> molecules and 11 Na.  I simply meant that I didn't understand the error
>> message since 17732 is divisible by 11.  I suspect that you didn't
>> choose
>> the correct group for solvent.
>>
>> Since you are a beginner may I suggest that you use one of the many
>> Gromacs tutorials available choosing one appropriate to what you are
>> trying
>> to do?  I am sure that you can find these easily enough with Google.
>>
>> Best regards?
>> Peter
>>
>> Sent from my iPhone
>>
>> > On 17 Mar 2016, at 12:27 PM, Pradip Kaur 
>> wrote:
>> >
>> > actually i m not getting how to proceed futher i m beginner to GROMACS
>> > it would be helpful if you can elaborate the process
>> >
>> >> On 17 March 2016 at 21:54, Pradip Kaur 
>> wrote:
>> >>
>> >> so should i go for sol molecules :1612
>> >> Na :11
>> >>
>> >>> On 17 March 2016 at 21:44, Peter Stern 
>> wrote:
>> >>>
>> >>> Missing atoms in GLU 474 is because the coordinates for the GLU side
>> >>> chain weren't resolved in the crystallographic data and aren't
>> included in
>> >>> the pdb file.  Long bonds are probably because of missing residues.
>> Check
>> >>> the pdb file for MISSING residues and atoms (listed in the header
>> >>> records).  Also, you can't just delete a residue and let Gromacs
>> think
>> that
>> >>> the preceding and following residues are connected (by an unphysical
>> "long"
>> >>> bond).  The same goes for missing residues in the pdb file.
>> >>>
>> >>> I hope that the net charge was -5.999 otherwise, why add Na ions.
>> And
>> as
>> >>> far as I know, 11*1612=17732.
>> >>>
>> >>> Peter Stern
>> >>>
>> >>> Sent from my iPad
>> >>>
>> >>> On 17 במרץ 2016, at 11:08, Pradip Kaur > > >>> kaur.pradip...@gmail.com>> wrote:
>> >>>
>> >>> i am currently working with 2bbo.pdb protein ,i have edited this
>> protein
>> >>> in
>> >>> Discovery studio 4.5 and deleted phenylalanine at 508 position , now
>> i
>> m
>> >>> running molecular dynamics simulation  in GROMACS 5.0.2 bt after
>> running
>> >>> pdb2gmx  with  GROMOS96 53a6 force field Water model :spc216 ,it is
>> >>> showing
>> >>>
>> >>> Warning: Long Bond (161-163 = 1.78456 nm)
>> >>>
>> >>> Warning: Long Bond (840-842 = 0.357037 nm)
>> >>>
>> >>> Warning: Long Bond (2237-2239 = 0.636287 nm)
>> >>>
>> >>>
>> >>>
>> >>> WARNING: atom CG is missing in residue GLU 474 in the pdb file
>> >>>
>> >>>
>> >>>
>> >>>
>> >>>
>> >>> WARNING: atom CD is missing in residue GLU 474 in the pdb file
>> >>>
>> >>>
>> >>>
>> >>>
>> >>>
>> >>> WARNING: atom OE1 is missing in residue GLU 474 in the pdb file
>> >>>
>> >>>
>> >>>
>> >>>
>> >>>
>> >>> WARNING: atom OE2 is missing in residue GLU 474 in the pdb file
>> >>>
>> >>>
>> >>>
>> >>>
>> >>>
>> >>> ---
>> >>>
>> >>> Program pdb2gmx, VERSION 5.0.2
>> >>>
>> >>> Source code file:
>> >>> /build/buildd/gromacs-5.0.2/src/gromacs/gmxpreprocess/pdb2top.cpp,
>> line:
>> >>> 1587
>> >>>
>> >>>
>> >>>
>> >>> Fatal error:
>> >>>
>> >>> There were 4 missing atoms in molecule Protein_chain_A, if you want
>> to
>> use
>> >>> this incomplete topology anyhow, use the option -missing
>> >>>
>> >>> For more information and tips for troubleshooting, please check the
>> >>> GROMACS
>> >>>
>> >>> website at http://www.gromacs.org/Documentation/Errors
>> >>>
>> >>>
>> >>> *But  after ignoring missing atoms ,when i am running grompp command
>> it
>> >>> shows that the system has non zero integral charge of 5.999.*
>> >>>
>> >>> *i have added command genion to neutalise the c

Re: [gmx-users] Extending the simulation

[jkrieger]

This page is now a little out of date. GROMACS 5 has replaced tbpconv with
gmx convert-tpr but otherwise the instructions are the same.

> http://www.gromacs.org/Documentation/How-tos/Extending_Simulations
>
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Re: [gmx-users] Extending the simulation

[jkrieger]

You'd use convert-tpr with the -until option, something like the following:

gmx convert-tpr -s md.tpr -f md.trr -until 10 -o md_new.tpr

See http://manual.gromacs.org/programs/gmx-convert-tpr.html for more
information.

Best wishes
James

> Dear Gromacs Usre
> I have performed a 10 ns MD simulation with Gromos 43A1 ff. Now I want to
> extend the simulation from 10 ns up to 100 ns. Would anyone tell me the
> most appropriate of continuing simulation?
> Thank You
>
> With Regards
> Suniba
>
> Sent from my iPhone
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Re: [gmx-users] PH of system

[jkrieger]

There is documentation on this at
http://www.gromacs.org/Documentation/How-tos/Constant_pH_Simulation but
the link to the mailing list there is out of date.

Also what about the method of Lee et al., J. Chem. Theory Comput., 2014 (
http://pubs.acs.org/doi/full/10.1021/ct500175m )? I guess once Enveloping
Distribution Sampling is implemented (Michael Shirts was planning this for
5.2 in Nov 2014:
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-developers/2014-November/008100.html
) then protonation with HREx and EDS could follow. Not being at all
involving in any developing myself I don't know how feasible this is or
how long it would take.

Best wishes
James

>
>
> On 12/20/15 11:36 PM, Sana Saeed wrote:
>> hi gmx usershow would i know the PH of the system, and how to manage the
>> value of PH, WHAT should i CHANGE to simulate a system at PH =2
>
> Check the archive; this comes up all the time.  Short answer: you can't
> really
> claim that any constant topology system without hydronium actually has a
> pH
> value.  What you can say is that you have protonated all relevant
> molecules at
> their predominant form at a given pH.
>
> -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
>
> ==
> --
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Re: [gmx-users] Multi-node Replica Exchange Segfault

[jkrieger]

You could try using a mixture of openmpi and thread-mpi. I have found when
linked replicas in multi-walker metadynamics that it only works if the
replicas have the same allocation of the cluster. In Sun Grid Engine, I'd
have the following in my submit scripts:

#$ -pe openmpi 2
#$ -l dedicated=20
export OMP_NUM_THREADS=20
mpirun -np $NSLOTS mdrun_mpi -deffnm metad -cpi metad -plumed plumed.dat
-multi 2

It's probably slightly different with PBS but you could try the equivalent
without the plumed and then with replex.

Best wishes
James

> Hi,
>
> I've never heard of such. You could try a multisim without -replex, to
> help
> diagnose.
>
> Mark
>
> On Fri, 30 Oct 2015 03:33 Barnett, James W  wrote:
>
>> Good evening here,
>>
>> I get a segmentation fault with my GROMACS 5.1 install only for replica
>> exchange
>> simulations right at the first successful exchange on a multi-node run.
>> Normal
>> simulations across multiple nodes work fine, and replica exchange
>> simulations on
>> one node work fine.
>>
>> I've reproduced the problem with just 2 replicas on 2 nodes with GPU's
>> disabled
>> (-nb cpu). Each node has 20 CPU's so I'm using 20 MPI ranks on each
>> (OpenMPI).
>>
>> I get a segfault right when the first exchange is successful.
>>
>> The only other error I get sometimes is that the Infiniband connection
>> timed out
>> retrying the communication between nodes at the exact same moment as the
>> segfault, but I don't get that every time, and it's usually with all
>> replicas
>> going (my goal is to do 30 replicas on 120 cpus). No other error logs,
>> and
>> mdrun's log does not indicate an error.
>>
>> PBS log: http://bit.ly/1P8Vs49
>> mdrun log: http://bit.ly/1RD0ViQ
>>
>> I'm currently troubleshooting this some with the sysadmin, but I wanted
>> to
>> check
>> to see if anyone has had a similar issue or any further steps to
>> troubleshoot.
>> I've also searched the mailing list and used my Google-fu, but it has
>> failed me
>> so far.
>>
>> Thanks for your help.
>>
>> --
>> James "Wes" Barnett, Ph.D. Candidate
>> Louisiana Board of Regents Fellow
>>
>> Chemical and Biomolecular Engineering
>> Tulane University
>> 341-B Lindy Boggs Center for Energy and Biotechnology
>> 6823 St. Charles Ave
>> New Orleans, Louisiana 70118-5674
>> jbarn...@tulane.edu
>> --
>> Gromacs Users mailing list
>>
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>> posting!
>>
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Re: [gmx-users] Problems installing gromacs 5.0.4 with plumed 2.1.2 for MPI

[jkrieger]

ok thanks Mark. Thread closed I guess.

Here's the updated solution in case other users refer to this thread for
the same problem. I've also updated the plumed google group thread with
the same solution.

1. configure/make/install plumed with addition of -fPIC to CFLAGS in
Makefile.conf before making (plumed-2.1.2 appears to need to be built in
the src directory)

tar -xvzf plumed-2.1.2.tgz
mv plumed-2.1.2 plumed-2.1.2-src
mkdir plumed-2.1.2-install
cd plumed-2.1.2-src
./configure --prefix=/lmb/home/jkrieger/
bin/plumed-2.1.2-install/ CC=mpicc CXX=mpicxx
manually add -fPIC to CFLAGS in Makefile.conf (done using vi)
make VERBOSE=1 | & tee m.txt
make install VERBOSE=1 | & tee mi.txt
update PATH and LD_LIBRARY_PATH (added to ~/.login on my system and
applied by logging out and back in again)

2. patch plumed onto gromacs in --runtime mode (as per recommendation of GB)

cd ~/bin
cp -r gromacs-5.0.4-src/ gromacs-5.0.4-src-plumed/
mkdir gromacs-5.0.4-build-plumed
mkdir gromacs-5.0.4-install-plumed
cd gromacs-5.0.4-src-plumed/
plumed patch -p --runtime

3. configure/make/install gromacs with separate src/build/install
directories (as per recommendation of MA) with removal of duplicate
reference to Plumed.o from
build-dir/src/gromacs/CMakeFiles/libgromacs.dir/link.txt (as per
recommendation of GB)

cd ../gromacs-5.0.4-build-plumed
cmake -DGMX_MPI=ON ../gromacs-5.0.4-src-plumed/ -DGMX_BUILD_OWN_FFTW=ON
-DCMAKE_INSTALL_PREFIX=/lmb/home/jkrieger/bin/gromacs-5.0.4-install-plumed
-DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpicxx
remove duplicate reference to Plumed.o from
build-dir/src/gromacs/CMakeFiles/libgromacs.dir/link.txt (again with vi)
make VERBOSE=1 | & tee m.txt
make install VERBOSE=1 | & tee mi.txt
update PATH and LD_LIBRARY_PATH (vi ~/.login, log out, log in again)

> Hi,
>
> That's why you use a wrapper compiler - if you run cmake and tell it to
> use
> the 1.8.5 wrapper compiler, you're good. But probably there will be no
> significant difference unless more recent MPI supports your network
> hardware better (in which case you should probably be using the MPI the
> sysadmins have set up).
>
> Mark
>
> On Wed, Jun 10, 2015 at 2:14 PM  wrote:
>
>> Yes that fixed it. I now have an mpi-aware version that works.
>>
>> I realise this is perhaps a separate issue now but it would be good to
>> use
>> the latest compiler version. My default is openmpi-1.5.4 and I could get
>> openmpi-1.8.5 now. How would I go about setting up wrappers for that?
>>
>> Many thanks again
>> James
>>
>> > Firstly the problem of finding PLUMED is now fixed.
>> >
>> > I appear to also have a problem that my mdrun_mpi isn't mpi-aware but
>> > rather starts an individual mdrun process on each node requested. I
>> think
>> > this might be related to this bug
>> http://redmine.gromacs.org/issues/572
>> > and am trying whether using the mpicc and mpicxx wrappers fixes it.
>> >
>> >> Unfortunately it's still not working. mdrun_mpi gives me the
>> following
>> >> error:
>> >>
>> >> Fatal error:
>> >> Plumed is not available. Check your PLUMED_KERNEL variable.
>> >>
>> >> Any ideas what's wrong now?
>> >>
>> >>> Here is the solution. Thanks to both Giovanni Bussi and Mark Abraham
>> >>> for
>> >>> your help.
>> >>>
>> >>> 0. configure/make/install mpi compilers (separate src, build and
>> >>> install
>> >>> directories are used as suggested by MA)
>> >>>
>> >>> tar -xvzfc mpich-3.1.4.tar.gz mpich-3.1.4-src
>> >>> mkdir mpich-3.1.4-build
>> >>> mkdir mpich-3.1.4-install
>> >>> cd mpich-3.1.4-build
>> >>> ../mpich-3.1.4-src/configure
>> >>> --prefix=/lmb/home/jkrieger/bin/mpich-3.1.4-install | & tee c.txt
>> >>> make VERBOSE=1 | & tee m.txt
>> >>> make install VERBOSE=1 | & tee mi.txt
>> >>>
>> >>> 1. configure/make/install plumed with addition of -fPIC to CFLAGS in
>> >>> Makefile.conf before making (plumed-2.1.2 appears to need to be
>> built
>> >>> in
>> >>> the src directory)
>> >>>
>> >>> tar -xvzfc plumed-2.1.2.tgz plumed-2.1.2-src
>> >>> mkdir plumed-2.1.2-install
>> >>> cd plumed-2.1.2-src
>> >>> ./configure --prefix=/lmb/home/jkrieger/bin/plumed-2.1.2-install/
>> >>> CC=/lmb/home/jkrieger/bin/mpich-3.1.4-install/bin/mpicc
>> >>> CXX=/lmb/home/jkrieger/bin/mpich-3.1.4-install/bin/

Re: [gmx-users] Problems installing gromacs 5.0.4 with plumed 2.1.2 for MPI

[jkrieger]

Yes that fixed it. I now have an mpi-aware version that works.

I realise this is perhaps a separate issue now but it would be good to use
the latest compiler version. My default is openmpi-1.5.4 and I could get
openmpi-1.8.5 now. How would I go about setting up wrappers for that?

Many thanks again
James

> Firstly the problem of finding PLUMED is now fixed.
>
> I appear to also have a problem that my mdrun_mpi isn't mpi-aware but
> rather starts an individual mdrun process on each node requested. I think
> this might be related to this bug http://redmine.gromacs.org/issues/572
> and am trying whether using the mpicc and mpicxx wrappers fixes it.
>
>> Unfortunately it's still not working. mdrun_mpi gives me the following
>> error:
>>
>> Fatal error:
>> Plumed is not available. Check your PLUMED_KERNEL variable.
>>
>> Any ideas what's wrong now?
>>
>>> Here is the solution. Thanks to both Giovanni Bussi and Mark Abraham
>>> for
>>> your help.
>>>
>>> 0. configure/make/install mpi compilers (separate src, build and
>>> install
>>> directories are used as suggested by MA)
>>>
>>> tar -xvzfc mpich-3.1.4.tar.gz mpich-3.1.4-src
>>> mkdir mpich-3.1.4-build
>>> mkdir mpich-3.1.4-install
>>> cd mpich-3.1.4-build
>>> ../mpich-3.1.4-src/configure
>>> --prefix=/lmb/home/jkrieger/bin/mpich-3.1.4-install | & tee c.txt
>>> make VERBOSE=1 | & tee m.txt
>>> make install VERBOSE=1 | & tee mi.txt
>>>
>>> 1. configure/make/install plumed with addition of -fPIC to CFLAGS in
>>> Makefile.conf before making (plumed-2.1.2 appears to need to be built
>>> in
>>> the src directory)
>>>
>>> tar -xvzfc plumed-2.1.2.tgz plumed-2.1.2-src
>>> mkdir plumed-2.1.2-install
>>> cd plumed-2.1.2-src
>>> ./configure --prefix=/lmb/home/jkrieger/bin/plumed-2.1.2-install/
>>> CC=/lmb/home/jkrieger/bin/mpich-3.1.4-install/bin/mpicc
>>> CXX=/lmb/home/jkrieger/bin/mpich-3.1.4-install/bin/mpicxx
>>> manually add -fPIC to CFLAGS in Makefile.conf (done using vi)
>>> make VERBOSE=1 | & tee m.txt
>>> make install VERBOSE=1 | & tee mi.txt
>>> update PATH and LD_LIBRARY_PATH (added to ~/.login on my system and
>>> applied by logging out and back in again)
>>>
>>> 2. patch plumed onto gromacs in --runtime mode (as per recommendation
>>> of
>>> GB)
>>>
>>> cd ~/bin
>>> cp -r gromacs-5.0.4-src/ gromacs-5.0.4-src-plumed/
>>> mkdir gromacs-5.0.4-build-plumed
>>> mkdir gromacs-5.0.4-install-plumed
>>> cd gromacs-5.0.4-src-plumed/
>>> plumed patch -p --runtime
>>>
>>> 3. configure/make/install gromacs with separate src/build/install
>>> directories (as per recommendation of MA) with removal of duplicate
>>> reference to Plumed.o from
>>> build-dir/src/gromacs/CMakeFiles/libgromacs.dir/link.txt (as per
>>> recommendation of GB)
>>>
>>> cd ../gromacs-5.0.4-build-plumed
>>> cmake -DGMX_MPI=ON ../gromacs-5.0.4-src-plumed/ -DGMX_BUILD_OWN_FFTW=ON
>>> -DCMAKE_INSTALL_PREFIX=/lmb/home/jkrieger/bin/gromacs-5.0.4-install-plumed
>>> -DCMAKE_C_COMPILER=/lmb/home/jkrieger/bin/mpich-3.1.4-install/bin/mpicc
>>> -DCMAKE_CXX_COMPILER=/lmb/home/jkrieger/bin/mpich-3.1.4-install/bin/mpicxx
>>> remove duplicate reference to Plumed.o from
>>> build-dir/src/gromacs/CMakeFiles/libgromacs.dir/link.txt (again with
>>> vi)
>>> make VERBOSE=1 | & tee m.txt
>>> make install VERBOSE=1 | & tee mi.txt
>>> update PATH and LD_LIBRARY_PATH (vi ~/.login, log out, log in again)
>>>
>>>> Thanks Mark. That seems to have worked. I will now try to do the same
>>>> with
>>>> Plumed.
>>>>
>>>>> Hi Mark,
>>>>>
>>>>> I will try that and let you know what happens.
>>>>>
>>>>> Thanks
>>>>> James
>>>>>
>>>>>> Hi,
>>>>>>
>>>>>> If you're trying to install into your source or build directory,
>>>>>> don't
>>>>>> do
>>>>>> that. You also seem to be running mpich from its build directory,
>>>>>> which
>>>>>> might be asking for trouble also. Unpack source in one place. Build
>>>>>> in
>>>>>> one
>>>>>> place, however that software prefers it. Install in yet another
>>>>>> pl

Re: [gmx-users] Problems installing gromacs 5.0.4 with plumed 2.1.2 for MPI

[jkrieger]

Firstly the problem of finding PLUMED is now fixed.

I appear to also have a problem that my mdrun_mpi isn't mpi-aware but
rather starts an individual mdrun process on each node requested. I think
this might be related to this bug http://redmine.gromacs.org/issues/572
and am trying whether using the mpicc and mpicxx wrappers fixes it.

> Unfortunately it's still not working. mdrun_mpi gives me the following
> error:
>
> Fatal error:
> Plumed is not available. Check your PLUMED_KERNEL variable.
>
> Any ideas what's wrong now?
>
>> Here is the solution. Thanks to both Giovanni Bussi and Mark Abraham for
>> your help.
>>
>> 0. configure/make/install mpi compilers (separate src, build and install
>> directories are used as suggested by MA)
>>
>> tar -xvzfc mpich-3.1.4.tar.gz mpich-3.1.4-src
>> mkdir mpich-3.1.4-build
>> mkdir mpich-3.1.4-install
>> cd mpich-3.1.4-build
>> ../mpich-3.1.4-src/configure
>> --prefix=/lmb/home/jkrieger/bin/mpich-3.1.4-install | & tee c.txt
>> make VERBOSE=1 | & tee m.txt
>> make install VERBOSE=1 | & tee mi.txt
>>
>> 1. configure/make/install plumed with addition of -fPIC to CFLAGS in
>> Makefile.conf before making (plumed-2.1.2 appears to need to be built in
>> the src directory)
>>
>> tar -xvzfc plumed-2.1.2.tgz plumed-2.1.2-src
>> mkdir plumed-2.1.2-install
>> cd plumed-2.1.2-src
>> ./configure --prefix=/lmb/home/jkrieger/bin/plumed-2.1.2-install/
>> CC=/lmb/home/jkrieger/bin/mpich-3.1.4-install/bin/mpicc
>> CXX=/lmb/home/jkrieger/bin/mpich-3.1.4-install/bin/mpicxx
>> manually add -fPIC to CFLAGS in Makefile.conf (done using vi)
>> make VERBOSE=1 | & tee m.txt
>> make install VERBOSE=1 | & tee mi.txt
>> update PATH and LD_LIBRARY_PATH (added to ~/.login on my system and
>> applied by logging out and back in again)
>>
>> 2. patch plumed onto gromacs in --runtime mode (as per recommendation of
>> GB)
>>
>> cd ~/bin
>> cp -r gromacs-5.0.4-src/ gromacs-5.0.4-src-plumed/
>> mkdir gromacs-5.0.4-build-plumed
>> mkdir gromacs-5.0.4-install-plumed
>> cd gromacs-5.0.4-src-plumed/
>> plumed patch -p --runtime
>>
>> 3. configure/make/install gromacs with separate src/build/install
>> directories (as per recommendation of MA) with removal of duplicate
>> reference to Plumed.o from
>> build-dir/src/gromacs/CMakeFiles/libgromacs.dir/link.txt (as per
>> recommendation of GB)
>>
>> cd ../gromacs-5.0.4-build-plumed
>> cmake -DGMX_MPI=ON ../gromacs-5.0.4-src-plumed/ -DGMX_BUILD_OWN_FFTW=ON
>> -DCMAKE_INSTALL_PREFIX=/lmb/home/jkrieger/bin/gromacs-5.0.4-install-plumed
>> -DCMAKE_C_COMPILER=/lmb/home/jkrieger/bin/mpich-3.1.4-install/bin/mpicc
>> -DCMAKE_CXX_COMPILER=/lmb/home/jkrieger/bin/mpich-3.1.4-install/bin/mpicxx
>> remove duplicate reference to Plumed.o from
>> build-dir/src/gromacs/CMakeFiles/libgromacs.dir/link.txt (again with vi)
>> make VERBOSE=1 | & tee m.txt
>> make install VERBOSE=1 | & tee mi.txt
>> update PATH and LD_LIBRARY_PATH (vi ~/.login, log out, log in again)
>>
>>> Thanks Mark. That seems to have worked. I will now try to do the same
>>> with
>>> Plumed.
>>>
>>>> Hi Mark,
>>>>
>>>> I will try that and let you know what happens.
>>>>
>>>> Thanks
>>>> James
>>>>
>>>>> Hi,
>>>>>
>>>>> If you're trying to install into your source or build directory,
>>>>> don't
>>>>> do
>>>>> that. You also seem to be running mpich from its build directory,
>>>>> which
>>>>> might be asking for trouble also. Unpack source in one place. Build
>>>>> in
>>>>> one
>>>>> place, however that software prefers it. Install in yet another
>>>>> place.
>>>>> Then
>>>>> use the installed version :-)
>>>>>
>>>>> Mark
>>>>>
>>>>> On Tue, Jun 9, 2015 at 5:15 PM  wrote:
>>>>>
>>>>>> You may be right. I get the same errors from trying to compile
>>>>>> non-PLUMED
>>>>>> normal GROMACS 5.0.4 as when I try with PLUMED (after removing
>>>>>> duplicate
>>>>>> instruction to link PLUMED).
>>>>>>
>>>>>> Make abruptly stops at this point with no clear error (using
>>>>>> VERBOSE=1).
>>>>>>
>>>>>> Linking CXX executable ../../b

Re: [gmx-users] Problems installing gromacs 5.0.4 with plumed 2.1.2 for MPI

[jkrieger]

Unfortunately it's still not working. mdrun_mpi gives me the following error:

Fatal error:
Plumed is not available. Check your PLUMED_KERNEL variable.

Any ideas what's wrong now?

> Here is the solution. Thanks to both Giovanni Bussi and Mark Abraham for
> your help.
>
> 0. configure/make/install mpi compilers (separate src, build and install
> directories are used as suggested by MA)
>
> tar -xvzfc mpich-3.1.4.tar.gz mpich-3.1.4-src
> mkdir mpich-3.1.4-build
> mkdir mpich-3.1.4-install
> cd mpich-3.1.4-build
> ../mpich-3.1.4-src/configure
> --prefix=/lmb/home/jkrieger/bin/mpich-3.1.4-install | & tee c.txt
> make VERBOSE=1 | & tee m.txt
> make install VERBOSE=1 | & tee mi.txt
>
> 1. configure/make/install plumed with addition of -fPIC to CFLAGS in
> Makefile.conf before making (plumed-2.1.2 appears to need to be built in
> the src directory)
>
> tar -xvzfc plumed-2.1.2.tgz plumed-2.1.2-src
> mkdir plumed-2.1.2-install
> cd plumed-2.1.2-src
> ./configure --prefix=/lmb/home/jkrieger/bin/plumed-2.1.2-install/
> CC=/lmb/home/jkrieger/bin/mpich-3.1.4-install/bin/mpicc
> CXX=/lmb/home/jkrieger/bin/mpich-3.1.4-install/bin/mpicxx
> manually add -fPIC to CFLAGS in Makefile.conf (done using vi)
> make VERBOSE=1 | & tee m.txt
> make install VERBOSE=1 | & tee mi.txt
> update PATH and LD_LIBRARY_PATH (added to ~/.login on my system and
> applied by logging out and back in again)
>
> 2. patch plumed onto gromacs in --runtime mode (as per recommendation of
> GB)
>
> cd ~/bin
> cp -r gromacs-5.0.4-src/ gromacs-5.0.4-src-plumed/
> mkdir gromacs-5.0.4-build-plumed
> mkdir gromacs-5.0.4-install-plumed
> cd gromacs-5.0.4-src-plumed/
> plumed patch -p --runtime
>
> 3. configure/make/install gromacs with separate src/build/install
> directories (as per recommendation of MA) with removal of duplicate
> reference to Plumed.o from
> build-dir/src/gromacs/CMakeFiles/libgromacs.dir/link.txt (as per
> recommendation of GB)
>
> cd ../gromacs-5.0.4-build-plumed
> cmake -DGMX_MPI=ON ../gromacs-5.0.4-src-plumed/ -DGMX_BUILD_OWN_FFTW=ON
> -DCMAKE_INSTALL_PREFIX=/lmb/home/jkrieger/bin/gromacs-5.0.4-install-plumed
> -DCMAKE_C_COMPILER=/lmb/home/jkrieger/bin/mpich-3.1.4-install/bin/mpicc
> -DCMAKE_CXX_COMPILER=/lmb/home/jkrieger/bin/mpich-3.1.4-install/bin/mpicxx
> remove duplicate reference to Plumed.o from
> build-dir/src/gromacs/CMakeFiles/libgromacs.dir/link.txt (again with vi)
> make VERBOSE=1 | & tee m.txt
> make install VERBOSE=1 | & tee mi.txt
> update PATH and LD_LIBRARY_PATH (vi ~/.login, log out, log in again)
>
>> Thanks Mark. That seems to have worked. I will now try to do the same
>> with
>> Plumed.
>>
>>> Hi Mark,
>>>
>>> I will try that and let you know what happens.
>>>
>>> Thanks
>>> James
>>>
>>>> Hi,
>>>>
>>>> If you're trying to install into your source or build directory, don't
>>>> do
>>>> that. You also seem to be running mpich from its build directory,
>>>> which
>>>> might be asking for trouble also. Unpack source in one place. Build in
>>>> one
>>>> place, however that software prefers it. Install in yet another place.
>>>> Then
>>>> use the installed version :-)
>>>>
>>>> Mark
>>>>
>>>> On Tue, Jun 9, 2015 at 5:15 PM  wrote:
>>>>
>>>>> You may be right. I get the same errors from trying to compile
>>>>> non-PLUMED
>>>>> normal GROMACS 5.0.4 as when I try with PLUMED (after removing
>>>>> duplicate
>>>>> instruction to link PLUMED).
>>>>>
>>>>> Make abruptly stops at this point with no clear error (using
>>>>> VERBOSE=1).
>>>>>
>>>>> Linking CXX executable ../../bin/gmx_mpi
>>>>> cd /lmb/home/jkrieger/bin/gromacs-mpi/src/programs && /usr/bin/cmake
>>>>> -E
>>>>> cmake_link_script CMakeFiles/gmx.dir/link.txt --verbose=1
>>>>> /lmb/home/jkrieger/bin/mpich-3.1.4-build/bin/mpicxx-mavx
>>>>> -Wextra
>>>>> -Wno-missing-field-initializers -Wpointer-arith -Wall
>>>>> -Wno-unused-function
>>>>>  -O3 -DNDEBUG -fomit-frame-pointer -funroll-all-loops
>>>>> -Wno-array-bounds
>>>>> CMakeFiles/gmx.dir/gmx.cpp.o
>>>>> CMakeFiles/gmx.dir/legacymodules.cpp.o
>>>>> CMakeFiles/mdrun_objlib.dir/mdrun/pme_loadbal.c.o
>>>>> CMakeFiles/mdrun_objlib.dir/mdrun/membed.c.o
>>>>

Re: [gmx-users] Problems installing gromacs 5.0.4 with plumed 2.1.2 for MPI

[jkrieger]

Here is the solution. Thanks to both Giovanni Bussi and Mark Abraham for
your help.

0. configure/make/install mpi compilers (separate src, build and install
directories are used as suggested by MA)

tar -xvzfc mpich-3.1.4.tar.gz mpich-3.1.4-src
mkdir mpich-3.1.4-build
mkdir mpich-3.1.4-install
cd mpich-3.1.4-build
../mpich-3.1.4-src/configure
--prefix=/lmb/home/jkrieger/bin/mpich-3.1.4-install | & tee c.txt
make VERBOSE=1 | & tee m.txt
make install VERBOSE=1 | & tee mi.txt

1. configure/make/install plumed with addition of -fPIC to CFLAGS in
Makefile.conf before making (plumed-2.1.2 appears to need to be built in
the src directory)

tar -xvzfc plumed-2.1.2.tgz plumed-2.1.2-src
mkdir plumed-2.1.2-install
cd plumed-2.1.2-src
./configure --prefix=/lmb/home/jkrieger/bin/plumed-2.1.2-install/
CC=/lmb/home/jkrieger/bin/mpich-3.1.4-install/bin/mpicc
CXX=/lmb/home/jkrieger/bin/mpich-3.1.4-install/bin/mpicxx
manually add -fPIC to CFLAGS in Makefile.conf (done using vi)
make VERBOSE=1 | & tee m.txt
make install VERBOSE=1 | & tee mi.txt
update PATH and LD_LIBRARY_PATH (added to ~/.login on my system and
applied by logging out and back in again)

2. patch plumed onto gromacs in --runtime mode (as per recommendation of GB)

cd ~/bin
cp -r gromacs-5.0.4-src/ gromacs-5.0.4-src-plumed/
mkdir gromacs-5.0.4-build-plumed
mkdir gromacs-5.0.4-install-plumed
cd gromacs-5.0.4-src-plumed/
plumed patch -p --runtime

3. configure/make/install gromacs with separate src/build/install
directories (as per recommendation of MA) with removal of duplicate
reference to Plumed.o from
build-dir/src/gromacs/CMakeFiles/libgromacs.dir/link.txt (as per
recommendation of GB)

cd ../gromacs-5.0.4-build-plumed
cmake -DGMX_MPI=ON ../gromacs-5.0.4-src-plumed/ -DGMX_BUILD_OWN_FFTW=ON
-DCMAKE_INSTALL_PREFIX=/lmb/home/jkrieger/bin/gromacs-5.0.4-install-plumed
-DCMAKE_C_COMPILER=/lmb/home/jkrieger/bin/mpich-3.1.4-install/bin/mpicc
-DCMAKE_CXX_COMPILER=/lmb/home/jkrieger/bin/mpich-3.1.4-install/bin/mpicxx
remove duplicate reference to Plumed.o from
build-dir/src/gromacs/CMakeFiles/libgromacs.dir/link.txt (again with vi)
make VERBOSE=1 | & tee m.txt
make install VERBOSE=1 | & tee mi.txt
update PATH and LD_LIBRARY_PATH (vi ~/.login, log out, log in again)

> Thanks Mark. That seems to have worked. I will now try to do the same with
> Plumed.
>
>> Hi Mark,
>>
>> I will try that and let you know what happens.
>>
>> Thanks
>> James
>>
>>> Hi,
>>>
>>> If you're trying to install into your source or build directory, don't
>>> do
>>> that. You also seem to be running mpich from its build directory, which
>>> might be asking for trouble also. Unpack source in one place. Build in
>>> one
>>> place, however that software prefers it. Install in yet another place.
>>> Then
>>> use the installed version :-)
>>>
>>> Mark
>>>
>>> On Tue, Jun 9, 2015 at 5:15 PM  wrote:
>>>
>>>> You may be right. I get the same errors from trying to compile
>>>> non-PLUMED
>>>> normal GROMACS 5.0.4 as when I try with PLUMED (after removing
>>>> duplicate
>>>> instruction to link PLUMED).
>>>>
>>>> Make abruptly stops at this point with no clear error (using
>>>> VERBOSE=1).
>>>>
>>>> Linking CXX executable ../../bin/gmx_mpi
>>>> cd /lmb/home/jkrieger/bin/gromacs-mpi/src/programs && /usr/bin/cmake
>>>> -E
>>>> cmake_link_script CMakeFiles/gmx.dir/link.txt --verbose=1
>>>> /lmb/home/jkrieger/bin/mpich-3.1.4-build/bin/mpicxx-mavx
>>>> -Wextra
>>>> -Wno-missing-field-initializers -Wpointer-arith -Wall
>>>> -Wno-unused-function
>>>>  -O3 -DNDEBUG -fomit-frame-pointer -funroll-all-loops
>>>> -Wno-array-bounds
>>>> CMakeFiles/gmx.dir/gmx.cpp.o
>>>> CMakeFiles/gmx.dir/legacymodules.cpp.o
>>>> CMakeFiles/mdrun_objlib.dir/mdrun/pme_loadbal.c.o
>>>> CMakeFiles/mdrun_objlib.dir/mdrun/membed.c.o
>>>> CMakeFiles/mdrun_objlib.dir/mdrun/runner.c.o
>>>> CMakeFiles/mdrun_objlib.dir/mdrun/md.c.o
>>>> CMakeFiles/mdrun_objlib.dir/mdrun/repl_ex.c.o
>>>> CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o
>>>> CMakeFiles/view_objlib.dir/view/view.cpp.o  -o ../../bin/gmx_mpi
>>>> -rdynamic
>>>> ../../lib/libgromacs_mpi.so.0.0.0 -fopenmp -ldl -lrt -lm -lz
>>>> ../contrib/fftw/fftwBuild-prefix/lib/libfftw3f.a -lblas -llapack
>>>> -lblas
>>>> -llapack -Wl,-rpath,/lmb/home/jkrieger/bin/gromacs-mpi/lib:
>>>> /usr/bin/cmake -E cmake_progress_report
>>>> /lmb/home/jkrieger/bi

Re: [gmx-users] Problems installing gromacs 5.0.4 with plumed 2.1.2 for MPI

[jkrieger]

Thanks Mark. That seems to have worked. I will now try to do the same with
Plumed.

> Hi Mark,
>
> I will try that and let you know what happens.
>
> Thanks
> James
>
>> Hi,
>>
>> If you're trying to install into your source or build directory, don't
>> do
>> that. You also seem to be running mpich from its build directory, which
>> might be asking for trouble also. Unpack source in one place. Build in
>> one
>> place, however that software prefers it. Install in yet another place.
>> Then
>> use the installed version :-)
>>
>> Mark
>>
>> On Tue, Jun 9, 2015 at 5:15 PM  wrote:
>>
>>> You may be right. I get the same errors from trying to compile
>>> non-PLUMED
>>> normal GROMACS 5.0.4 as when I try with PLUMED (after removing
>>> duplicate
>>> instruction to link PLUMED).
>>>
>>> Make abruptly stops at this point with no clear error (using
>>> VERBOSE=1).
>>>
>>> Linking CXX executable ../../bin/gmx_mpi
>>> cd /lmb/home/jkrieger/bin/gromacs-mpi/src/programs && /usr/bin/cmake -E
>>> cmake_link_script CMakeFiles/gmx.dir/link.txt --verbose=1
>>> /lmb/home/jkrieger/bin/mpich-3.1.4-build/bin/mpicxx-mavx-Wextra
>>> -Wno-missing-field-initializers -Wpointer-arith -Wall
>>> -Wno-unused-function
>>>  -O3 -DNDEBUG -fomit-frame-pointer -funroll-all-loops
>>> -Wno-array-bounds
>>> CMakeFiles/gmx.dir/gmx.cpp.o CMakeFiles/gmx.dir/legacymodules.cpp.o
>>> CMakeFiles/mdrun_objlib.dir/mdrun/pme_loadbal.c.o
>>> CMakeFiles/mdrun_objlib.dir/mdrun/membed.c.o
>>> CMakeFiles/mdrun_objlib.dir/mdrun/runner.c.o
>>> CMakeFiles/mdrun_objlib.dir/mdrun/md.c.o
>>> CMakeFiles/mdrun_objlib.dir/mdrun/repl_ex.c.o
>>> CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o
>>> CMakeFiles/view_objlib.dir/view/view.cpp.o  -o ../../bin/gmx_mpi
>>> -rdynamic
>>> ../../lib/libgromacs_mpi.so.0.0.0 -fopenmp -ldl -lrt -lm -lz
>>> ../contrib/fftw/fftwBuild-prefix/lib/libfftw3f.a -lblas -llapack -lblas
>>> -llapack -Wl,-rpath,/lmb/home/jkrieger/bin/gromacs-mpi/lib:
>>> /usr/bin/cmake -E cmake_progress_report
>>> /lmb/home/jkrieger/bin/gromacs-mpi/CMakeFiles
>>> [100%] Built target gmx
>>> /usr/bin/cmake -E cmake_progress_start
>>> /lmb/home/jkrieger/bin/gromacs-mpi/CMakeFiles 0
>>>
>>> Make install then complains that it cannot find gmx_mpi:
>>>
>>> CMake Error at src/programs/cmake_install.cmake:42 (FILE):
>>>   file INSTALL cannot find
>>> "/lmb/home/jkrieger/bin/gromacs-mpi/bin/gmx_mpi".
>>> Call Stack (most recent call first):
>>>   src/cmake_install.cmake:40 (INCLUDE)
>>>   cmake_install.cmake:49 (INCLUDE)
>>>
>>> > Hi,
>>> >
>>> > Anything. I think I understood that you can't install non-PLUMED
>>> normal
>>> > GROMACS in MPI mode, in which case the main suspect is your MPI
>>> > infrastructure, e.g. it was compiled with a different / incompatible
>>> > compiler from the one you're using now.
>>> >
>>> > Mark
>>> >
>>> > On Tue, Jun 9, 2015 at 4:23 PM  wrote:
>>> >
>>> >> Hi Mark,
>>> >>
>>> >> Sorry I missed your message as I had forgotten I needed to enable
>>> >> receiving messages. What MPI test program did you have in mind?
>>> >>
>>> >> Best wishes
>>> >> James
>>> >>
>>> >> > More details are available on the plumed forum google group at
>>> >> >
>>> >>
>>> https://groups.google.com/forum/?utm_medium=email&utm_source=footer#!msg/plumed-users/stlK9-kaa6A/jSm8rOON_xsJ
>>> >> >
>>> >> >> Hi,
>>> >> >>
>>> >> >> I have successfully installed plumed-2.1.2 (I believe with MPI
>>> >> >> capabilities) and patched it onto gromacs-5.0.4, I am now trying
>>> to
>>> >> >> install the gromacs and it's not working. Here are my errors from
>>> >> make:
>>> >> >>
>>> >> >> collect2: error: ld returned 1 exit status
>>> >> >> src/gromacs/CMakeFiles/libgromacs.dir/build.make:22956: recipe
>>> for
>>> >> >> target
>>> >> >> 'lib/libgromacs_mpi.so.0.0.0' failed
>>> >> >> make[2]: *** [lib/libgromacs_mp

Re: [gmx-users] Problems installing gromacs 5.0.4 with plumed 2.1.2 for MPI

[jkrieger]

Hi Mark,

I will try that and let you know what happens.

Thanks
James

> Hi,
>
> If you're trying to install into your source or build directory, don't do
> that. You also seem to be running mpich from its build directory, which
> might be asking for trouble also. Unpack source in one place. Build in one
> place, however that software prefers it. Install in yet another place.
> Then
> use the installed version :-)
>
> Mark
>
> On Tue, Jun 9, 2015 at 5:15 PM  wrote:
>
>> You may be right. I get the same errors from trying to compile
>> non-PLUMED
>> normal GROMACS 5.0.4 as when I try with PLUMED (after removing duplicate
>> instruction to link PLUMED).
>>
>> Make abruptly stops at this point with no clear error (using VERBOSE=1).
>>
>> Linking CXX executable ../../bin/gmx_mpi
>> cd /lmb/home/jkrieger/bin/gromacs-mpi/src/programs && /usr/bin/cmake -E
>> cmake_link_script CMakeFiles/gmx.dir/link.txt --verbose=1
>> /lmb/home/jkrieger/bin/mpich-3.1.4-build/bin/mpicxx-mavx-Wextra
>> -Wno-missing-field-initializers -Wpointer-arith -Wall
>> -Wno-unused-function
>>  -O3 -DNDEBUG -fomit-frame-pointer -funroll-all-loops  -Wno-array-bounds
>> CMakeFiles/gmx.dir/gmx.cpp.o CMakeFiles/gmx.dir/legacymodules.cpp.o
>> CMakeFiles/mdrun_objlib.dir/mdrun/pme_loadbal.c.o
>> CMakeFiles/mdrun_objlib.dir/mdrun/membed.c.o
>> CMakeFiles/mdrun_objlib.dir/mdrun/runner.c.o
>> CMakeFiles/mdrun_objlib.dir/mdrun/md.c.o
>> CMakeFiles/mdrun_objlib.dir/mdrun/repl_ex.c.o
>> CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o
>> CMakeFiles/view_objlib.dir/view/view.cpp.o  -o ../../bin/gmx_mpi
>> -rdynamic
>> ../../lib/libgromacs_mpi.so.0.0.0 -fopenmp -ldl -lrt -lm -lz
>> ../contrib/fftw/fftwBuild-prefix/lib/libfftw3f.a -lblas -llapack -lblas
>> -llapack -Wl,-rpath,/lmb/home/jkrieger/bin/gromacs-mpi/lib:
>> /usr/bin/cmake -E cmake_progress_report
>> /lmb/home/jkrieger/bin/gromacs-mpi/CMakeFiles
>> [100%] Built target gmx
>> /usr/bin/cmake -E cmake_progress_start
>> /lmb/home/jkrieger/bin/gromacs-mpi/CMakeFiles 0
>>
>> Make install then complains that it cannot find gmx_mpi:
>>
>> CMake Error at src/programs/cmake_install.cmake:42 (FILE):
>>   file INSTALL cannot find
>> "/lmb/home/jkrieger/bin/gromacs-mpi/bin/gmx_mpi".
>> Call Stack (most recent call first):
>>   src/cmake_install.cmake:40 (INCLUDE)
>>   cmake_install.cmake:49 (INCLUDE)
>>
>> > Hi,
>> >
>> > Anything. I think I understood that you can't install non-PLUMED
>> normal
>> > GROMACS in MPI mode, in which case the main suspect is your MPI
>> > infrastructure, e.g. it was compiled with a different / incompatible
>> > compiler from the one you're using now.
>> >
>> > Mark
>> >
>> > On Tue, Jun 9, 2015 at 4:23 PM  wrote:
>> >
>> >> Hi Mark,
>> >>
>> >> Sorry I missed your message as I had forgotten I needed to enable
>> >> receiving messages. What MPI test program did you have in mind?
>> >>
>> >> Best wishes
>> >> James
>> >>
>> >> > More details are available on the plumed forum google group at
>> >> >
>> >>
>> https://groups.google.com/forum/?utm_medium=email&utm_source=footer#!msg/plumed-users/stlK9-kaa6A/jSm8rOON_xsJ
>> >> >
>> >> >> Hi,
>> >> >>
>> >> >> I have successfully installed plumed-2.1.2 (I believe with MPI
>> >> >> capabilities) and patched it onto gromacs-5.0.4, I am now trying
>> to
>> >> >> install the gromacs and it's not working. Here are my errors from
>> >> make:
>> >> >>
>> >> >> collect2: error: ld returned 1 exit status
>> >> >> src/gromacs/CMakeFiles/libgromacs.dir/build.make:22956: recipe for
>> >> >> target
>> >> >> 'lib/libgromacs_mpi.so.0.0.0' failed
>> >> >> make[2]: *** [lib/libgromacs_mpi.so.0.0.0] Error 1
>> >> >> CMakeFiles/Makefile2:1948: recipe for target
>> >> >> 'src/gromacs/CMakeFiles/libgromacs.dir/all' failed
>> >> >> make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
>> >> >> Makefile:146: recipe for target 'all' failed
>> >> >> make: *** [all] Error 2
>> >> >>
>> >> >> I have successfully installed the latest gcc compilers and tried
>> to
>> >> te

Re: [gmx-users] Problems installing gromacs 5.0.4 with plumed 2.1.2 for MPI

[jkrieger]

You may be right. I get the same errors from trying to compile non-PLUMED
normal GROMACS 5.0.4 as when I try with PLUMED (after removing duplicate
instruction to link PLUMED).

Make abruptly stops at this point with no clear error (using VERBOSE=1).

Linking CXX executable ../../bin/gmx_mpi
cd /lmb/home/jkrieger/bin/gromacs-mpi/src/programs && /usr/bin/cmake -E
cmake_link_script CMakeFiles/gmx.dir/link.txt --verbose=1
/lmb/home/jkrieger/bin/mpich-3.1.4-build/bin/mpicxx-mavx-Wextra
-Wno-missing-field-initializers -Wpointer-arith -Wall -Wno-unused-function
 -O3 -DNDEBUG -fomit-frame-pointer -funroll-all-loops  -Wno-array-bounds  
CMakeFiles/gmx.dir/gmx.cpp.o CMakeFiles/gmx.dir/legacymodules.cpp.o
CMakeFiles/mdrun_objlib.dir/mdrun/pme_loadbal.c.o
CMakeFiles/mdrun_objlib.dir/mdrun/membed.c.o
CMakeFiles/mdrun_objlib.dir/mdrun/runner.c.o
CMakeFiles/mdrun_objlib.dir/mdrun/md.c.o
CMakeFiles/mdrun_objlib.dir/mdrun/repl_ex.c.o
CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o
CMakeFiles/view_objlib.dir/view/view.cpp.o  -o ../../bin/gmx_mpi -rdynamic
../../lib/libgromacs_mpi.so.0.0.0 -fopenmp -ldl -lrt -lm -lz
../contrib/fftw/fftwBuild-prefix/lib/libfftw3f.a -lblas -llapack -lblas
-llapack -Wl,-rpath,/lmb/home/jkrieger/bin/gromacs-mpi/lib:
/usr/bin/cmake -E cmake_progress_report
/lmb/home/jkrieger/bin/gromacs-mpi/CMakeFiles
[100%] Built target gmx
/usr/bin/cmake -E cmake_progress_start
/lmb/home/jkrieger/bin/gromacs-mpi/CMakeFiles 0

Make install then complains that it cannot find gmx_mpi:

CMake Error at src/programs/cmake_install.cmake:42 (FILE):
  file INSTALL cannot find "/lmb/home/jkrieger/bin/gromacs-mpi/bin/gmx_mpi".
Call Stack (most recent call first):
  src/cmake_install.cmake:40 (INCLUDE)
  cmake_install.cmake:49 (INCLUDE)

> Hi,
>
> Anything. I think I understood that you can't install non-PLUMED normal
> GROMACS in MPI mode, in which case the main suspect is your MPI
> infrastructure, e.g. it was compiled with a different / incompatible
> compiler from the one you're using now.
>
> Mark
>
> On Tue, Jun 9, 2015 at 4:23 PM  wrote:
>
>> Hi Mark,
>>
>> Sorry I missed your message as I had forgotten I needed to enable
>> receiving messages. What MPI test program did you have in mind?
>>
>> Best wishes
>> James
>>
>> > More details are available on the plumed forum google group at
>> >
>> https://groups.google.com/forum/?utm_medium=email&utm_source=footer#!msg/plumed-users/stlK9-kaa6A/jSm8rOON_xsJ
>> >
>> >> Hi,
>> >>
>> >> I have successfully installed plumed-2.1.2 (I believe with MPI
>> >> capabilities) and patched it onto gromacs-5.0.4, I am now trying to
>> >> install the gromacs and it's not working. Here are my errors from
>> make:
>> >>
>> >> collect2: error: ld returned 1 exit status
>> >> src/gromacs/CMakeFiles/libgromacs.dir/build.make:22956: recipe for
>> >> target
>> >> 'lib/libgromacs_mpi.so.0.0.0' failed
>> >> make[2]: *** [lib/libgromacs_mpi.so.0.0.0] Error 1
>> >> CMakeFiles/Makefile2:1948: recipe for target
>> >> 'src/gromacs/CMakeFiles/libgromacs.dir/all' failed
>> >> make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
>> >> Makefile:146: recipe for target 'all' failed
>> >> make: *** [all] Error 2
>> >>
>> >> I have successfully installed the latest gcc compilers and tried to
>> tell
>> >> gromacs to use them with the following command (not sure if this is
>> >> right):
>> >> ccmake ../gromacs-5.0.4/ -DGMX_BUILD_OWN_FFTW=ON
>> >> -DCMAKE_C_COMPILER=/lmb/home/jkrieger/bin/gcc-5.1.0-build/bin/gcc
>> >>
>> >> In any case I get similar errors using the default compilers on my
>> >> system.
>> >>
>> >> I am installing on a front-end node of our cluster at the LMB, which
>> has
>> >> a
>> >> shared filesystem.
>> >>
>> >> Please let me know if there's anything else I need to tell you so
>> that
>> >> you
>> >> can help.
>> >>
>> >> Many thanks
>> >> James
>> >>
>> >
>> >
>> >
>>
>>
>> --
>> 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
>> 

Re: [gmx-users] Problems installing gromacs 5.0.4 with plumed 2.1.2 for MPI

[jkrieger]

I have GROMACS 4.6 installed in MPI mode and have been using it for some
time. I haven't actually tried installing GROMACS 5.0 without PLUMED. I'll
try that now and let you know if that works.

> Hi,
>
> Anything. I think I understood that you can't install non-PLUMED normal
> GROMACS in MPI mode, in which case the main suspect is your MPI
> infrastructure, e.g. it was compiled with a different / incompatible
> compiler from the one you're using now.
>
> Mark
>
> On Tue, Jun 9, 2015 at 4:23 PM  wrote:
>
>> Hi Mark,
>>
>> Sorry I missed your message as I had forgotten I needed to enable
>> receiving messages. What MPI test program did you have in mind?
>>
>> Best wishes
>> James
>>
>> > More details are available on the plumed forum google group at
>> >
>> https://groups.google.com/forum/?utm_medium=email&utm_source=footer#!msg/plumed-users/stlK9-kaa6A/jSm8rOON_xsJ
>> >
>> >> Hi,
>> >>
>> >> I have successfully installed plumed-2.1.2 (I believe with MPI
>> >> capabilities) and patched it onto gromacs-5.0.4, I am now trying to
>> >> install the gromacs and it's not working. Here are my errors from
>> make:
>> >>
>> >> collect2: error: ld returned 1 exit status
>> >> src/gromacs/CMakeFiles/libgromacs.dir/build.make:22956: recipe for
>> >> target
>> >> 'lib/libgromacs_mpi.so.0.0.0' failed
>> >> make[2]: *** [lib/libgromacs_mpi.so.0.0.0] Error 1
>> >> CMakeFiles/Makefile2:1948: recipe for target
>> >> 'src/gromacs/CMakeFiles/libgromacs.dir/all' failed
>> >> make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
>> >> Makefile:146: recipe for target 'all' failed
>> >> make: *** [all] Error 2
>> >>
>> >> I have successfully installed the latest gcc compilers and tried to
>> tell
>> >> gromacs to use them with the following command (not sure if this is
>> >> right):
>> >> ccmake ../gromacs-5.0.4/ -DGMX_BUILD_OWN_FFTW=ON
>> >> -DCMAKE_C_COMPILER=/lmb/home/jkrieger/bin/gcc-5.1.0-build/bin/gcc
>> >>
>> >> In any case I get similar errors using the default compilers on my
>> >> system.
>> >>
>> >> I am installing on a front-end node of our cluster at the LMB, which
>> has
>> >> a
>> >> shared filesystem.
>> >>
>> >> Please let me know if there's anything else I need to tell you so
>> that
>> >> you
>> >> can help.
>> >>
>> >> Many thanks
>> >> James
>> >>
>> >
>> >
>> >
>>
>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
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>>
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>> send a mail to gmx-users-requ...@gromacs.org.
>>
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Re: [gmx-users] Problems installing gromacs 5.0.4 with plumed 2.1.2 for MPI

[jkrieger]

Hi Mark,

Sorry I missed your message as I had forgotten I needed to enable
receiving messages. What MPI test program did you have in mind?

Best wishes
James

> More details are available on the plumed forum google group at
> https://groups.google.com/forum/?utm_medium=email&utm_source=footer#!msg/plumed-users/stlK9-kaa6A/jSm8rOON_xsJ
>
>> Hi,
>>
>> I have successfully installed plumed-2.1.2 (I believe with MPI
>> capabilities) and patched it onto gromacs-5.0.4, I am now trying to
>> install the gromacs and it's not working. Here are my errors from make:
>>
>> collect2: error: ld returned 1 exit status
>> src/gromacs/CMakeFiles/libgromacs.dir/build.make:22956: recipe for
>> target
>> 'lib/libgromacs_mpi.so.0.0.0' failed
>> make[2]: *** [lib/libgromacs_mpi.so.0.0.0] Error 1
>> CMakeFiles/Makefile2:1948: recipe for target
>> 'src/gromacs/CMakeFiles/libgromacs.dir/all' failed
>> make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
>> Makefile:146: recipe for target 'all' failed
>> make: *** [all] Error 2
>>
>> I have successfully installed the latest gcc compilers and tried to tell
>> gromacs to use them with the following command (not sure if this is
>> right):
>> ccmake ../gromacs-5.0.4/ -DGMX_BUILD_OWN_FFTW=ON
>> -DCMAKE_C_COMPILER=/lmb/home/jkrieger/bin/gcc-5.1.0-build/bin/gcc
>>
>> In any case I get similar errors using the default compilers on my
>> system.
>>
>> I am installing on a front-end node of our cluster at the LMB, which has
>> a
>> shared filesystem.
>>
>> Please let me know if there's anything else I need to tell you so that
>> you
>> can help.
>>
>> Many thanks
>> James
>>
>
>
>


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Re: [gmx-users] Problems installing gromacs 5.0.4 with plumed 2.1.2 for MPI

[jkrieger]

More details are available on the plumed forum google group at
https://groups.google.com/forum/?utm_medium=email&utm_source=footer#!msg/plumed-users/stlK9-kaa6A/jSm8rOON_xsJ

> Hi,
>
> I have successfully installed plumed-2.1.2 (I believe with MPI
> capabilities) and patched it onto gromacs-5.0.4, I am now trying to
> install the gromacs and it's not working. Here are my errors from make:
>
> collect2: error: ld returned 1 exit status
> src/gromacs/CMakeFiles/libgromacs.dir/build.make:22956: recipe for target
> 'lib/libgromacs_mpi.so.0.0.0' failed
> make[2]: *** [lib/libgromacs_mpi.so.0.0.0] Error 1
> CMakeFiles/Makefile2:1948: recipe for target
> 'src/gromacs/CMakeFiles/libgromacs.dir/all' failed
> make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
> Makefile:146: recipe for target 'all' failed
> make: *** [all] Error 2
>
> I have successfully installed the latest gcc compilers and tried to tell
> gromacs to use them with the following command (not sure if this is
> right):
> ccmake ../gromacs-5.0.4/ -DGMX_BUILD_OWN_FFTW=ON
> -DCMAKE_C_COMPILER=/lmb/home/jkrieger/bin/gcc-5.1.0-build/bin/gcc
>
> In any case I get similar errors using the default compilers on my system.
>
> I am installing on a front-end node of our cluster at the LMB, which has a
> shared filesystem.
>
> Please let me know if there's anything else I need to tell you so that you
> can help.
>
> Many thanks
> James
>


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[gmx-users] Problems installing gromacs 5.0.4 with plumed 2.1.2 for MPI

[jkrieger]

Hi,

I have successfully installed plumed-2.1.2 (I believe with MPI
capabilities) and patched it onto gromacs-5.0.4, I am now trying to
install the gromacs and it's not working. Here are my errors from make:

collect2: error: ld returned 1 exit status
src/gromacs/CMakeFiles/libgromacs.dir/build.make:22956: recipe for target
'lib/libgromacs_mpi.so.0.0.0' failed
make[2]: *** [lib/libgromacs_mpi.so.0.0.0] Error 1
CMakeFiles/Makefile2:1948: recipe for target
'src/gromacs/CMakeFiles/libgromacs.dir/all' failed
make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
Makefile:146: recipe for target 'all' failed
make: *** [all] Error 2

I have successfully installed the latest gcc compilers and tried to tell
gromacs to use them with the following command (not sure if this is
right):
ccmake ../gromacs-5.0.4/ -DGMX_BUILD_OWN_FFTW=ON
-DCMAKE_C_COMPILER=/lmb/home/jkrieger/bin/gcc-5.1.0-build/bin/gcc

In any case I get similar errors using the default compilers on my system.

I am installing on a front-end node of our cluster at the LMB, which has a
shared filesystem.

Please let me know if there's anything else I need to tell you so that you
can help.

Many thanks
James

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[gmx-users] parametrization of GABA for charmm27

[jkrieger]

Hi,

I have parametrized gamma-aminobutyric acid (GABA; three-letter residue
code ABU) for charmm27, which lacked it. This is essentially a hybrid of
glutamate and lysine parameters. I thought this would be a reasonable
starting point especially seeing as there is an overlap point at Glu CB
and Lys CD, which share a charge of -0.18

I would like to add my changes to the topologies archive
(http://www.gromacs.org/Downloads/User_contributions/Molecule_topologies)
for the benefit of other users but the "attach file" link is greyed out.
Instead I copy them into this email.

There are, however, some problems where pdb2gmx changes things (at least
version 4.6.1 which I am using):
1. The charges of the carboxyl group are changed such that the topology
doesn't end up with 0 charge. This needs to be manually corrected at
present.
2. It also adds 3 extra hydrogens to the amino group (a total of 6 rather
than 3), which also have to be removed manually from the topology and
output structure. This requires additionally that the atoms be renumbered
to continue consecutively.
3. As GABA lacks a carboxyl group on the amino carbon (CA) it has two
hydrogens, which are correctly added. However the topology says that it is
CT1 rather than CT2. This needs to manually corrected too, especially
seeing as no N-CT1-H Urey-Bradley parameters exist.

Here are the lines I added into aminoacids.rtp

[ ABU ]
 [ atoms ]
N   NH3 -0.30   0
H1  HC  0.331
H2  HC  0.332
H3  HC  0.333
CA  CT2 0.214
HA1 HA  0.055
HA2 HA  0.056
CB  CT2 -0.18   7
HB1 HA  0.098
HB2 HA  0.099
CG  CT2 -0.28   10
HG1 HA  0.0911
HG2 HA  0.0912
C   CC  0.6213
OT1 OC  -0.76   14
OT2 OC  -0.76   15
 [ bonds ]
CB  CA
CG  CB
C   CG
OT2 C
N   H1
N   H2
N   H3
N   CA
CA  HA1
CA  HA2
CB  HB1
CB  HB2
CG  HG1
CG  HG2
C   OT1
 [ impropers ]
C   CG  OT2 OT1

and here are the lines I added into aminoacids.hdb

ABU 4
3   4   H   N   CA  CB
2   6   HA  CA  N   CB
2   6   HB  CB  CA  CG
2   6   HG  CG  CB  C

Perhaps someone can see from these lines what is causing the strange
problems above..

Best wishes
James

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Re: [gmx-users] Is version 5.0 generating portable binaries?

[jkrieger]

Can you not find out what acceleration types you cluster has from the cluster 
admin and select nodes appropriately? I do this on our cluster by providing 
qsub with the flag -l node_type=m620

On 31 Jan 2014, at 01:40, Mark Abraham  wrote:

> On Jan 30, 2014 11:57 PM, "Raffaella D'Auria"  wrote:
>> 
>> Hello All,
>> 
>> I have just performed a fresh installation of gromacs version 4.6.5 on a
> heterogeneous linux cluster (running centos 6.4) . After the installation I
> see that the binaries, for say mdrun,  work on all the machines with
> hardware similar to the one on which they were installed (namely AMD
> processor such as: Quad-Core AMD Opteron Processor 2354) but produce an
> "illegal instruction (core dumped)" when run on nodes with intel processors
> (such as: Intel Xeon CPU E5335  @ 2.00GHz).
>> 
>> As suggested in the documentation (
> http://www.gromacs.org/Documentation/Acceleration_and_parallelization#CPU_acceleration.3a_SSE.2c_AVX.2c_etc)
> I have tried to compile with GMX_CPU_ACCELERATION set to "none" (I have
> also turned down the optimization levels) with always the same result
> (illegal instruction) across different hardware.
>> 
>> Is this expected behavior? If so will the binaries of version 5.* have
> the same portability problem?
> 
> In short, yes, and yes. While discussions like
> http://redmine.gromacs.org/issues/1165 have taken place, nobody has decided
> to commit time to solving this, because the only benefit comes when the
> target machine architecture is variable, unknown, and there is no local
> mechanism in place to call the correct mdrun. This painful situation is
> partly created by choosing to have a  heterogeneous cluster... In 5.0 you
> will be able to compile for SSE4.1 and avoid RDTSC with the distributable
> build option, but this is wasting the capabilities of the AMD processors. A
> second GROMACS install, together with a recommended run script that chooses
> the mdrun binary based on the node name / whatever should be a reasonable
> solution.
> 
> Mark
> 
>> One more thing the situation described above occurs with both the gnu
> 4.4.7 compiler and the intel 13.1.1.
>> 
>> Any feedback would be greatly appreciated.
>> 
>> Thanks,
>> 
>> Raffaella.
>> 
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Re: [gmx-users] future of shell completions in GROMACS

[jkrieger]

ok. I suppose I can try.

> On Wed, Jan 22, 2014 at 5:50 PM,   wrote:
>> I +1 shell completions too. It would be ok for me too if they were only
>> in
>> bash. I think my default shell on the cluster may be tcsh but I can
>> change
>> it to bash if necessary.
>>
>> I'd be happy to try helping to implement it but I don't have much
>> experience in C or C++ (I mainly use Python).
>
> You need no C/C++ knowledge to help with this,  it's all bash!
> See:
> http://redmine.gromacs.org/projects/gromacs/repository/revisions/master/entry/scripts/completion.bash
> http://redmine.gromacs.org/projects/gromacs/repository/revisions/master/entry/scripts/completion.csh
> http://redmine.gromacs.org/projects/gromacs/repository/revisions/master/entry/scripts/completion.zsh
>
>
>>
>>> On Tue, Jan 21, 2014 at 10:23 AM, Djurre de Jong-Bruinink
>>>  wrote:

>Do you use this feature?
>Do you use this feature with a shell other than bash?

 Yes, I use this feature and missing it would be a great loss to my
 workflow. However, I only use it in bash. Is the auto-completion
 planned
 to work for files only, or also for the tools (e.g.: gmx gro
 auto-completes to gmx grompp). I noticed this doesn't work in the
 beta-version either.
>>>
>>> I guess that doesn't work because the auto-completion has not been
>>> adapted from 4.6 to 5.0. IMO we should fix this, but it'd be great to
>>> get a few more +1-s and helping hands, otherwise there is a risk of it
>>> getting deprecated which would be a big loss.
>>>


 On a slightly related issue: the enviroment variable "GMX_NO_CREDITS"
 doesn't work anymore in gmx5b. That made my work in the terminal a lot
 easier too (Not that I think you guys don't deserve the credits!). Is
 that planned to be reimplemented? I also find the template/layout of
 the
 "credits-section" less structured and appealing than in the old
 version.
>>>
>>> Do you mean less structured and less appealing? Could you please file
>>> a redmine issue about GMX_NO_CREDITS and whatever else you;d like to
>>> mention?
>>>

 Best regards/groetnis,
 Djurre


 
 Djurre H. de Jong, PhD
 Westfälische Wilhelms-Universität Münster
 Institut für Physikalische Chemie
 Corrensstr. 28/30
 D-48149 Münster
 *
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>>>
>>
>>
>>
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Re: [gmx-users] future of shell completions in GROMACS

[jkrieger]

I +1 shell completions too. It would be ok for me too if they were only in
bash. I think my default shell on the cluster may be tcsh but I can change
it to bash if necessary.

I'd be happy to try helping to implement it but I don't have much
experience in C or C++ (I mainly use Python).

> On Tue, Jan 21, 2014 at 10:23 AM, Djurre de Jong-Bruinink
>  wrote:
>>
>>>Do you use this feature?
>>>Do you use this feature with a shell other than bash?
>>
>> Yes, I use this feature and missing it would be a great loss to my
>> workflow. However, I only use it in bash. Is the auto-completion planned
>> to work for files only, or also for the tools (e.g.: gmx gro
>> auto-completes to gmx grompp). I noticed this doesn't work in the
>> beta-version either.
>
> I guess that doesn't work because the auto-completion has not been
> adapted from 4.6 to 5.0. IMO we should fix this, but it'd be great to
> get a few more +1-s and helping hands, otherwise there is a risk of it
> getting deprecated which would be a big loss.
>
>>
>>
>> On a slightly related issue: the enviroment variable "GMX_NO_CREDITS"
>> doesn't work anymore in gmx5b. That made my work in the terminal a lot
>> easier too (Not that I think you guys don't deserve the credits!). Is
>> that planned to be reimplemented? I also find the template/layout of the
>> "credits-section" less structured and appealing than in the old version.
>
> Do you mean less structured and less appealing? Could you please file
> a redmine issue about GMX_NO_CREDITS and whatever else you;d like to
> mention?
>
>>
>> Best regards/groetnis,
>> Djurre
>>
>>
>> 
>> Djurre H. de Jong, PhD
>> Westfälische Wilhelms-Universität Münster
>> Institut für Physikalische Chemie
>> Corrensstr. 28/30
>> D-48149 Münster
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Re: [gmx-users] question

[jkrieger]

Thanks. I hadn't noticed that option.

> Instead of such a complicated script, I would use 'g_select -os', which
> gives you the same output without any post-processing. Whether this
> matches
> what the original poster wanted, or whether g_rdf is more suitable,
> depends
> on what they want to count.
>
> Best regards,
> Teemu
>
> On Tue, Jan 21, 2014 at 2:04 PM,  wrote:
>
>> Here is my python script as promised:
>>
>> # select filenames for reading and writing
>> fr = open('chainA_T78-waters_index.ndx','r')
>> fw = open('chainA_T78-waters_counts.xvg','w')
>>
>> line = fr.readline()
>> t = line.split('_')[-1].split()[0]
>> c = 0
>>
>> for line in fr:
>> if line.find('[') == -1:
>> c += len(line.split())
>> else:
>> fw.write(t + ' ' + str(c) + '\n')
>> t = line.split('_')[-1].split()[0]
>> c = 0
>>
>> fw.write(t + ' ' + str(c) + '\n')
>>
>> fr.close()
>> fw.close()
>>
>> It reads in a file from g_select that looks as follows
>> [ chain_A_T78_waters_0.000 ]
>> 45170 45172 55565 55566 55567 217685 217686 217688 217689 217690 217709
>> 217710 217711 355868 355870
>> 380249 380250 380251
>> [ chain_A_T78_waters_2.000 ]
>> 55565 55566 55567 217686 217688 217689 217690 217709 217710 217711
>> 289964
>> 355868 355870 380249 380250
>> 380251
>> [ chain_A_T78_waters_4.000 ]
>> 45170 45171 45172 55565 55566 55567 217688 217689 217690 217709 217710
>> 217711 355869 367615 380249
>> 380250 380251
>>
>> and write out a file with counts that looks like this that xmgrace can
>> read
>> 0.000 18
>> 2.000 16
>> 4.000 17
>>
>> Best wishes
>> James
>>
>> > I have no experience with g_rdf but that looks like it might work if
>> you
>> > only want the average number. Anyhow I'm writing the script to count
>> my
>> > g_select output now and I'll send it to you soon. This script should
>> allow
>> > the number to be plotted over time.
>> >
>> > Best wishes
>> > James
>> >
>> >> Dear Jkrieger
>> >>
>> >> Thanks for your attention.
>> >>
>> >> I have index file containing 2 group which are my interest.
>> >>
>> >> Unfortunately, I am beginner in scripting and I have no long time.
>> >> I should do this analysis as soon as possible. Please if you write
>> such
>> >> a
>> >> script, send me it.
>> >>
>> >> Is g_rdf -cn appropriate for my case?
>>
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Re: [gmx-users] question

[jkrieger]

Here is my python script as promised:

# select filenames for reading and writing
fr = open('chainA_T78-waters_index.ndx','r')
fw = open('chainA_T78-waters_counts.xvg','w')

line = fr.readline()
t = line.split('_')[-1].split()[0]
c = 0

for line in fr:
if line.find('[') == -1:
c += len(line.split())
else:
fw.write(t + ' ' + str(c) + '\n')
t = line.split('_')[-1].split()[0]
c = 0

fw.write(t + ' ' + str(c) + '\n')

fr.close()
fw.close()

It reads in a file from g_select that looks as follows
[ chain_A_T78_waters_0.000 ]
45170 45172 55565 55566 55567 217685 217686 217688 217689 217690 217709
217710 217711 355868 355870
380249 380250 380251
[ chain_A_T78_waters_2.000 ]
55565 55566 55567 217686 217688 217689 217690 217709 217710 217711 289964
355868 355870 380249 380250
380251
[ chain_A_T78_waters_4.000 ]
45170 45171 45172 55565 55566 55567 217688 217689 217690 217709 217710
217711 355869 367615 380249
380250 380251

and write out a file with counts that looks like this that xmgrace can read
0.000 18
2.000 16
4.000 17

Best wishes
James

> I have no experience with g_rdf but that looks like it might work if you
> only want the average number. Anyhow I'm writing the script to count my
> g_select output now and I'll send it to you soon. This script should allow
> the number to be plotted over time.
>
> Best wishes
> James
>
>> Dear Jkrieger
>>
>> Thanks for your attention.
>>
>> I have index file containing 2 group which are my interest.
>>
>> Unfortunately, I am beginner in scripting and I have no long time.
>> I should do this analysis as soon as possible. Please if you write such
>> a
>> script, send me it.
>>
>> Is g_rdf -cn appropriate for my case?
>>
>> Best wishes
>> --
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>>
>
>
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Re: [gmx-users] question

[jkrieger]

I have no experience with g_rdf but that looks like it might work if you
only want the average number. Anyhow I'm writing the script to count my
g_select output now and I'll send it to you soon. This script should allow
the number to be plotted over time.

Best wishes
James

> Dear Jkrieger
>
> Thanks for your attention.
>
> I have index file containing 2 group which are my interest.
>
> Unfortunately, I am beginner in scripting and I have no long time.
> I should do this analysis as soon as possible. Please if you write such a
> script, send me it.
>
> Is g_rdf -cn appropriate for my case?
>
> Best wishes
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Re: [gmx-users] question

[jkrieger]

Yes you can ask for any distance with g_select.

On 21 Jan 2014, at 08:10, Andrew Bostick  wrote:

> Dear all
> 
> My aim of the number of neighbours (NS) is different from Neighbor
> Searching (nstlist and rlist) in mdp file.
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Re: [gmx-users] question

[jkrieger]

I think g_select would be the best tool for this. It can output index groups 
containing this information for each frame. You can then write a script to 
count these and/or extract the group of all neighbours. I might try and write 
such a script myself in the next few days then I'll send it out.

On 21 Jan 2014, at 08:05, Andrew Bostick  wrote:

> Dear all
> 
> I want to obtain number of atoms in a first group which are located in
> special distance of the second group.
> 
> How to do this? Which tool of gromacs can do it? In fact, I want to obtain
> number of neighbours (NS).
> 
> Any help will highly appreciated.
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Re: [gmx-users] name problem

[jkrieger]

I think you can't. People have asked similar questions before. You need to
rename the lipids yourself to 3 letter names e.g. POC and POG.

> Hello:
>
> I found a problem of lipids name when I use editconf each time. My
> lipids name are: POPC and POPG. When I run command:
>
> editconf -f em.gro -o em.pdb
>
> the name of my lipids for both POPC and POPG are "POP". I am just
> wondering how can we solve this problem by exporting the full name of
> lipids?
>
> thank you very much
> Albert
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Re: [gmx-users] editconf

[jkrieger]

In terms of cutoffs and self-interaction, this is probably fine (you have
2.2nm between copies of your peptide). In terms of aggregation this
probably too big unless you have multiple molecules in each copy.

> Dear GMX-Users,
>
>   For understanding the aggregation propensity of the
> peptide I did a 1 us md simulation with periodic boundary. I defined a
> triclinic box around my peptide using editconf. The command I used is the
> following
> editconf -f tau_pep.gro -bt triclinic -d 1.1 -princ -o box.gro.
>  Here -d 1.1 make any problems in the simulation?Is the value is
> appropriate?
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Re: [gmx-users] restarting MD after error in the middle of trajectory

[jkrieger]

Perhaps you should restart without a cpt like you would before version 4.
You could use tpbconv with -time 5 (ps) to make a new tpr which you
then use with mdrun instead. Hopefully that helps.

Best wishes
James

> Hi,
>
> I have strange situation.
> I am running MD with 4 replicas and when I recently checked the trajectory
> with gmxcheck in one replica I got this error:
>
> Fatal error:
> Magic Number Error in XTC file (read 0, should be 1995)
>
>
> It is arround 50ns of the simulation, and right now I have 120ns.
> I would like to restart my simulation from the part before 50ns but I am
> not
> sure how to do this because my cpt file are written after 120ns...
> Can I generate new cpt file based on the part of the simulation before
> 50ns?
> Thanks for any suggestions.
> Best,
>
> tomek
>
> --
> View this message in context:
> http://gromacs.5086.x6.nabble.com/restarting-MD-after-error-in-the-middle-of-trajectory-tp5013632.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
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Re: [gmx-users] Restarting crashed run

[jkrieger]

You do need to give -cpi state.cpt

It is not part of the default set.

> Dear gromacs users
>
> I have a small query regarding restarting crashed run. If I have given
> following command:
> mdrun -s topol.tpr
> i.e. without giving -cpi state.cpt , But my folder contains state.cpt,
> does
> it automatically takes this input file from the folder?
> Also, does the same thing holds true for extending simulations
> (no crashed runs)?
> Does this depends on version also (say from gromacs 4.0.7 till 4.6.3)?
>
> Thanks in advance
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Re: [gmx-users] Bin files of g_sham

[jkrieger]

You're not asking it to read the bin index file in your command. Maybe that 
explains what you're seeing?

On 18 Dec 2013, at 13:51, Ankita Naithani  wrote:

> Hi Lloyd,
> 
> So, my input to g_sham is a file with following lines:
> 
> @title "2D projection of trajectory"
> @xaxis  label "projection on eigenvector 1 (nm)"
> @yaxis  label "projection on eigenvector 2 (nm)"
> @TYPE xy
>   0.167500.18278
>  -0.01448   -0.14834
>  -0.327570.22259
>  -0.338320.63817
> 
> This file is named AM_12.xvg
> 
> and my command line is g_sham -f AM_12.xvg -ls AM_FEL_12.xpm
> 
> My bin index file has the following lines:
> 
> [ 18 ]
> 7105
> [ 19 ]
> 7104
> [ 46 ]
> 7124
> [ 48 ]
> 7123
> [ 49 ]
> 7106
> [ 50 ]
> 6497
> 6498
> [ 51 ]
> 6499
> 6500
> [ 52 ]
> 6496
> 7103
> [ 53 ]
> 7102
> [ 55 ]
> 6672
> [ 75 ]
> 5745
> 5749
> and so on.
> 
> I am not sure how can I look at the default binwidth.
> 
> Kind regards,
> 
> Ankita
> 
> 
> On Tue, Dec 17, 2013 at 6:03 PM, lloyd riggs  wrote:
> 
>> 
>> You need to explain what you are doing better, what you want to do, and
>> show your input (command line, .xvg lines of input and output as example)
>> and you might get more help on here.  If you read the -h from g_sham, it is
>> making a single plot from your input, and in this case your .xpm would be a
>> matrix with bins on a 2D surface with points taken across the entire run,
>> as an example of what I mean. I believe you can also use a single line
>> (time, energy as column 2), and get a single line out as well, with a
>> meaningless "landscape" still put out as .xpm, etc...look at your binwidth
>> default, input and what you want out is all I could say at this point.  You
>> might be trying to do something else however...
>> 
>> Stephan
>> *Gesendet:* Dienstag, 17. Dezember 2013 um 08:38 Uhr
>> 
>> *Von:* "Ankita Naithani" 
>> *An:* "Discussion list for GROMACS users" 
>> *Betreff:* Re: [gmx-users] Bin files of g_sham
>> I would like to add that maybe the bins store Frame numbers. Because I seem
>> to have around 21000 frames and I guess I am unable to see a number higher
>> than that. Apologies for the confusion about earlier number. So, in this
>> case if I want a confirmation at a particular frame number, how should I go
>> about that? Could you please help me with that?
>> 
>> Kind regards,
>> 
>> Ankita
>> 
>> 
>> On Tue, Dec 17, 2013 at 7:20 AM, Ankita Naithani
>> wrote:
>> 
>>> Hi Llyod,
>>> 
>>> Thank you for your reply. I actually wanted to extract frames
>>> corresponding to the g_sham output. The input for g_sham in my case was
>>> column 1 had time points, column 2 and column 3 had Principal component 1
>>> and Principal component 2 respectively. So, the binning which has been
>>> done, i.e. if I say that the bin number 786 has the following few numbers
>>> like : 3876, 9870, 22002 etc. These should technically correspond to the
>>> time points right which I can then dump using trjconv too maybe.
>>> 
>>> Also, I am a little confused because if the bins have all the time
>> points,
>>> I don't seem to find the time points uptil the end of simulation in that
>>> case i.e. I am unable to see higher time scale. My simulation was for
>> 48ns
>>> and had 3fs time step. I am unable to trace anything beyond 22000 or
>> 23000
>>> number in my bins.
>>> 
>>> I hope you could help me solve this confusion.
>>> 
>>> Kind regards,
>>> 
>>> Ankita
>>> 
>>> 
>>> On Sun, Dec 15, 2013 at 11:17 PM, lloyd riggs 
>> wrote:
>>> 
 
 I will attempt an answer, however there might be a better response. It
 depends on your input .xvg (what the first column is) and what you are
 telling it to do (defualt is time), and if these correspond to your time
 frames (can be timepoint or siply frame # I believe). g_sham seems (to
>> me)
 to work like a comand line spread sheet manipulator with some built in
 functions. If you want a particular frame from a trajectory time point,
 then use g_traj with the first/last set to the frame you want but
>> there's
 also 2 other tools that do this the same way...
 
 Stephan Watkins
 *Gesendet:* Sonntag, 15. Dezember 2013 um 14:49 Uhr
 *Von:* "Ankita Naithani" 
 *An:* "Discussion list for GROMACS users" 
 *Betreff:* [gmx-users] Bin files of g_sham
>> 
 Hi,
 
 I had a query regarding the bin files generated by g_sham.
 Does the bin index contain timepoints? i.e. there are 1024 bins so each
 bin
 has a number of time points? And supposes bin 756 has numbers like 3876,
 20020, 7896 so these would all correspond to time and we could then dump
 the representative frame corresponding to these time points?
 
 I am a little confused as to what is stored in the bins? Timepoints or
 frame number and then alternatively how to get the representative
 frame/snapshot stored at that specific bin number.
 
 Kind regards,
 
 --
 Ankita Naithani
 --
 Gromacs Users maili

Re: [gmx-users] selection around circle

[jkrieger]

Does it make sense to install gromacs 5.0 beta for analysing a simulation from 
4.6.x?

On 18 Dec 2013, at 05:17, Venkat Reddy  wrote:

> Hi,
> I have had used 5.0 beta version and as far as I know, "gmx gangle"
> supports the output from g_select.
> 
> 
> On Wed, Dec 18, 2013 at 6:39 AM, Justin Lemkul  wrote:
> 
>> 
>> 
>> On 12/17/13 7:43 PM, jkrie...@mrc-lmb.cam.ac.uk wrote:
>> 
>>> Thanks Justin,
>>> 
>>> I have tried this and I can a new index file that has an item for each
>>> frame with atoms that match the selection. How do I create a single index
>>> item and combine it into the main index file for use with other tools such
>>> as g_hbond?
>> The output of g_select is not fully compatible with any Gromacs tool, at
>> least in any pre-5.0 version.  Given that I have had not had time yet to
>> fully investigate the current beta, hopefully someone else can say whether
>> or not the g_select output is now fully supported by other tools.
>> 
>> -Justin
>> 
>> 
>> Best wishes
>>> James
>>> 
>>> On 18 Dec 2013, at 00:14, Justin Lemkul  wrote:
>>> 
>>> 
 
 On 12/17/13 1:55 PM, jkrie...@mrc-lmb.cam.ac.uk wrote:
 
> I think g_select does something like this. I am trying to do something
> similar: make a selection of water within 5A or so of a residue in my
> protein. Also need help please.
 
 The examples at the end of g_select -select 'help all' pretty well cover
 most of these situations.  What have you tried?  What has it given you?
 Something like:
 
 same residue as resname SOL and within 0.5 of residue X
 
 provided that residue X is defined within an .ndx file provided on the
 command, line should work.  Disclaimer: this is just off the cuff, but
 probably pretty close.
 
 -Justin
 
 Dear Gmx Users,
>> 
>> I have my carbon nanotube (lenght z axis) with proteins attached to
>> it. I
>> wish to collect RDF of given type of amino acids away from the surface
>> in
>> two dimensions (xy). Z axis does not interest me. That would make a
>> circle
>> then. My question: how to make a specific index group of this circle?
>> Any
>> ideas appreciated.
>> 
>> Steven
>> --
>> 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.
 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
 
 ==
 --
 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.
>> 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
>> 
>> ==
>> --
>> Gromacs Users mailing list
>> 
>> * Please search the archive at http://www.gromacs.org/
>> Support/Mailing_Lists/GMX-Users_List before posting!
>> 
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>> send a mail to gmx-users-requ...@gromacs.org.
> 
> 
> 
> -- 
> With Best Wishes
> Venkat Reddy Chirasani
> PhD student
> Laboratory of Computational Biophysics
> Department of Biotechnology
> IIT Madras
> Chennai
> INDIA-600036
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Re: [gmx-users] selection around circle

[jkrieger]

Thanks Justin,

I have tried this and I can a new index file that has an item for each frame 
with atoms that match the selection. How do I create a single index item and 
combine it into the main index file for use with other tools such as g_hbond?

Best wishes
James

On 18 Dec 2013, at 00:14, Justin Lemkul  wrote:

> 
> 
> On 12/17/13 1:55 PM, jkrie...@mrc-lmb.cam.ac.uk wrote:
>> I think g_select does something like this. I am trying to do something
>> similar: make a selection of water within 5A or so of a residue in my
>> protein. Also need help please.
> 
> The examples at the end of g_select -select 'help all' pretty well cover most 
> of these situations.  What have you tried?  What has it given you?  Something 
> like:
> 
> same residue as resname SOL and within 0.5 of residue X
> 
> provided that residue X is defined within an .ndx file provided on the 
> command, line should work.  Disclaimer: this is just off the cuff, but 
> probably pretty close.
> 
> -Justin
> 
>>> Dear Gmx Users,
>>> 
>>> I have my carbon nanotube (lenght z axis) with proteins attached to it. I
>>> wish to collect RDF of given type of amino acids away from the surface in
>>> two dimensions (xy). Z axis does not interest me. That would make a circle
>>> then. My question: how to make a specific index group of this circle? Any
>>> ideas appreciated.
>>> 
>>> Steven
>>> --
>>> 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.
> 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
> 
> ==
> -- 
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Re: [gmx-users] Gromos DPPC bilayer: different results for 4.0.7 and 4.6.5

[jkrieger]

You can't attach things to the list. Perhaps you could upload it to
dropbox or something and give us a link.

> Thank you all for your comments! It's interesting that Patrick ran into
> the same issues just a few days earlier.
>
> Following your suggestions, I started some simulations with the
> "Reaction-Field-nec" coulombtype. So far those have run for only about 30
> nanoseconds, but based on the attached graph I would assume that they will
> still result in an area per lipid that is lower than that obtained with
> Gromacs 4.0.7.  I will update the bug report on redmine once the
> simulations have progressed a little more.
>
> What would the next step be trying to debug this issue? Is it possible to
> output only the various components of the forces (in particular, those
> induced by the reaction field)?
>
> Best,
>
>   Lutz
>
>
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Re: [gmx-users] selection around circle

[jkrieger]

I think g_select does something like this. I am trying to do something
similar: make a selection of water within 5A or so of a residue in my
protein. Also need help please.

> Dear Gmx Users,
>
> I have my carbon nanotube (lenght z axis) with proteins attached to it. I
> wish to collect RDF of given type of amino acids away from the surface in
> two dimensions (xy). Z axis does not interest me. That would make a circle
> then. My question: how to make a specific index group of this circle? Any
> ideas appreciated.
>
> Steven
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
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Re: [gmx-users] How to find the mutation effect?

[jkrieger]

How long are you simulating for? Have you looked at the rmsf?

On 15 Dec 2013, at 18:42, xiao  wrote:

> Dear all,
> 
> I am doing a MD on a mutant protein which is unstable from exprient. However, 
> i found no difference between the wild type and the mutant protein from md, 
> the structure and the rmsd are very similar in the mutant and the wild type.
> 
> Can anyone tell me how to tackle this problem?
> 
> Best regards
> 
> Fugui
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Re: [gmx-users] constraining protein in the box

[jkrieger]

This is probably a visualisation problem not a simulation problem. You may
just need to process the simulation with trjconv using -pbc nojump.

> Sir,
>
> I completed a 400 ns MD simulation. But in some part of the trajectory
> my protein is just out side the box I selected (triclinic). Is there any
> option in gromacs to constrain my protein in box during simulation.
>
>
>
> Thanks in advance ..
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Re: [gmx-users] the crashed run

[jkrieger]

_prev.cpt might be ok. I think it writes those in case the current cpt causes 
problems

On 8 Dec 2013, at 09:57, Mahboobeh Eslami  wrote:

> hi GMX users
> i use gromacs 4.6.3 double precision for protein ligand complex during the 20 
> ns. my run crashed, I'm not sure that restart my run from cpt file or run a 
> new production.
> is the result of  started again run a reliable like a non crashed run.
> 
> thanks for your help
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Re: [gmx-users] exclusions

[jkrieger]

You can maybe do up to triplet or quadruplets - it talks about doing that
for default Lennard-Jones. You can modify the python script to extra loops
e.g. over k. A key point is probably also to keep all exclusions the same
length. Again I don't know much about this but thought I'd try to be
helpful.

> Thank you a lot for this. As it states in the manual
> [ exclusions ]
> 1 2 3
> 2 1 3
> 3 1 2
>
> But this makes repeats so I tried:
> [exclusions]
> 1 2 3 4 5
> 2 3 4 5
> 3 4 5
> 4 5
>
> Both not working and the simulation crashes. I think there is too much
> data...
>
> Steven
>
>
> On Fri, Dec 6, 2013 at 12:44 PM,  wrote:
>
>> I may be completely wrong but I think each line should be a pair with no
>> pair represented in reverse e.g.
>> 1 2
>> 1 3
>> 2 3
>> 1 4
>> 2 4
>> 3 4
>> and so on.
>>
>> Here's a python script to do this for your 2516 atoms. Indentation is
>> part
>> of the code and the standard indentation is 4 presses of the spacebar.
>>
>> f = open('exclusions.txt')
>> f.write('[ exclusions ]')
>> for i in range(2516):
>> for j in range(2516):
>> f.write(str(i+1, j+1))
>> f.close()
>>
>> i+1 and j+1 are used because python starts counting at 0 and atoms are
>> counted starting at 1.
>>
>> You can use standard command line editing tools such as cat to join this
>> into a file with other sections.
>>
>> > I generated the [ exclusions ] so that the maximum characters
>> correspond
>> > to
>> > 4000 - line break is made after this. So I generated the tpr file with
>> > grompp and when running:
>> >
>> > Reading file md.tpr, VERSION 4.5.5 (single precision)
>> > Starting 8 threads
>> > Making 2D domain decomposition 4 x 2 x 1
>> > *** glibc detected *** mdrun: realloc(): invalid next size:
>> > 0x2b2d801eebd0 ***
>> > === Backtrace: =
>> > /lib64/libc.so.6[0x300f873b64]
>> > /lib64/libc.so.6(realloc+0x102)[0x300f875c92]
>> >
>> /usr/local/gromacs-4.5.5/lib/libgmx.so.6(save_realloc+0x4d)[0x2b2d792dc04d]
>> >
>> /usr/local/gromacs-4.5.5/lib/libmd.so.6(dd_make_local_top+0x1252)[0x2b2d78fcce82]
>> >
>> /usr/local/gromacs-4.5.5/lib/libmd.so.6(dd_partition_system+0x183c)[0x2b2d78f4005c]
>> > mdrun(do_md+0x771)[0x41cb61]
>> > mdrun(mdrunner+0xa3d)[0x40ce4d]
>> > mdrun[0x40dd96]
>> > /usr/local/gromacs-4.5.5/lib/libgmx.so.6[0x2b2d794fa14e]
>> > /lib64/libpthread.so.0[0x301080683d]
>> > /lib64/libc.so.6(clone+0x6d)[0x300f8d526d]
>> > === Memory map: 
>> > 0040-00432000 r-xp  00:1d 149136
>> > /rvol/cpse-apps/RHEL5-x86_64/gromacs-4.5.5/bin/mdrun
>> > 00631000-00633000 rwxp 00031000 00:1d 149136
>> > /rvol/cpse-apps/RHEL5-x86_64/gromacs-4.5.5/bin/mdrun
>> > 00633000-00634000 rwxp 00633000 00:00 0
>> > 1c12c000-1c3dc000 rwxp 1c12c000 00:00 0
>> > [heap]
>> > 300f40-300f41c000 r-xp  08:02 43548681
>> > /lib64/ld-2.5.so
>> > 300f61c000-300f61d000 r-xp 0001c000 08:02 43548681
>> > /lib64/ld-2.5.so
>> > 300f61d000-300f61e000 rwxp 0001d000 08:02 43548681
>> > /lib64/ld-2.5.so
>> > 300f80-300f94f000 r-xp  08:02 43548690
>> > /lib64/libc-2.5.so
>> > 300f94f000-300fb4f000 ---p 0014f000 08:02 43548690
>> > /lib64/libc-2.5.so
>> > 300fb4f000-300fb53000 r-xp 0014f000 08:02 43548690
>> > /lib64/libc-2.5.so
>> > 300fb53000-300fb54000 rwxp 00153000 08:02 43548690
>> > /lib64/libc-2.5.so
>> > 300fb54000-300fb59000 rwxp 300fb54000 00:00 0
>> > 300fc0-300fc82000 r-xp  08:02 43549057
>> > /lib64/libm-2.5.so
>> > 300fc82000-300fe81000 ---p 00082000 08:02 43549057
>> > /lib64/libm-2.5.so
>> > 300fe81000-300fe82000 r-xp 00081000 08:02 43549057
>> > /lib64/libm-2.5.so
>> > 300fe82000-300fe83000 rwxp 00082000 08:02 43549057
>> > /lib64/libm-2.5.so
>> > 301000-3010002000 r-xp  08:02 43548960
>> > /lib64/libdl-2.5.so
>> > 3010002000-3010202000 ---p 2000 08:02 43548960
>> > /lib64/libdl-2.5.so
>> > 3010202000-3010203000 r-xp 2000 08:02 43548960
>> > /lib64/libdl-2.5.so
>> > 3010203000-3010204000 rwxp 3000 08:02 43548960
>> > /lib64/libdl-2.5.so
>> > 301040-3010414000 r-xp  08:02 43548948
>> > /lib64/libz.so.1.2.3
>> > 3010414000-3010613000 ---p 00014000 08:02 43548948
>> > /lib64/libz.so.1.2.3
>> > 3010613000-3010614000 rwxp 00013000 08:02 43548948
>> > /lib64/libz.so.1.2.3
>> > 301080-3010816000 r-xp  08:02 43548875
>> > /lib64/libpthread-2.5.so
>> > 3010816000-3010a16000 ---p 00016000 08:02 43548875
>> > /lib64/libpthread-2.5.so
>> > 3010a16000-3010a17000 r-xp 00016000 08:02 43548875
>> > /lib64/libpthread-2.5.so
>> > 3010a17000-3010a18000 rwxp 00017000 08:02 43548875
>> > /lib64/libpthread-2.5.so
>> > 3010a18000-3010a1c000 rwxp 3010a18000 00:00 0
>> > 3018a0-3018b34000 r-xp  08:02 28578909
>> > /usr/lib64/libxml2.so.2.6.26
>> > 3018b34000-3018d34000 ---p 00134000 08:02 28578909
>> > /usr/lib64/libxml2.so.2.6.26
>> > 3018d34000-3018d3d000 rwxp 00134000 08:02 28578909
>> > /usr/lib64/libxml2.so.2.6.26
>> > 3018d3d000-3018d3e000 rwxp 3018d3d000 00:00 0
>> > 301da0-301da0d000 r-xp 

Re: [gmx-users] exclusions

[jkrieger]

I may be completely wrong but I think each line should be a pair with no
pair represented in reverse e.g.
1 2
1 3
2 3
1 4
2 4
3 4
and so on.

Here's a python script to do this for your 2516 atoms. Indentation is part
of the code and the standard indentation is 4 presses of the spacebar.

f = open('exclusions.txt')
f.write('[ exclusions ]')
for i in range(2516):
for j in range(2516):
f.write(str(i+1, j+1))
f.close()

i+1 and j+1 are used because python starts counting at 0 and atoms are
counted starting at 1.

You can use standard command line editing tools such as cat to join this
into a file with other sections.

> I generated the [ exclusions ] so that the maximum characters correspond
> to
> 4000 - line break is made after this. So I generated the tpr file with
> grompp and when running:
>
> Reading file md.tpr, VERSION 4.5.5 (single precision)
> Starting 8 threads
> Making 2D domain decomposition 4 x 2 x 1
> *** glibc detected *** mdrun: realloc(): invalid next size:
> 0x2b2d801eebd0 ***
> === Backtrace: =
> /lib64/libc.so.6[0x300f873b64]
> /lib64/libc.so.6(realloc+0x102)[0x300f875c92]
> /usr/local/gromacs-4.5.5/lib/libgmx.so.6(save_realloc+0x4d)[0x2b2d792dc04d]
> /usr/local/gromacs-4.5.5/lib/libmd.so.6(dd_make_local_top+0x1252)[0x2b2d78fcce82]
> /usr/local/gromacs-4.5.5/lib/libmd.so.6(dd_partition_system+0x183c)[0x2b2d78f4005c]
> mdrun(do_md+0x771)[0x41cb61]
> mdrun(mdrunner+0xa3d)[0x40ce4d]
> mdrun[0x40dd96]
> /usr/local/gromacs-4.5.5/lib/libgmx.so.6[0x2b2d794fa14e]
> /lib64/libpthread.so.0[0x301080683d]
> /lib64/libc.so.6(clone+0x6d)[0x300f8d526d]
> === Memory map: 
> 0040-00432000 r-xp  00:1d 149136
> /rvol/cpse-apps/RHEL5-x86_64/gromacs-4.5.5/bin/mdrun
> 00631000-00633000 rwxp 00031000 00:1d 149136
> /rvol/cpse-apps/RHEL5-x86_64/gromacs-4.5.5/bin/mdrun
> 00633000-00634000 rwxp 00633000 00:00 0
> 1c12c000-1c3dc000 rwxp 1c12c000 00:00 0
> [heap]
> 300f40-300f41c000 r-xp  08:02 43548681
> /lib64/ld-2.5.so
> 300f61c000-300f61d000 r-xp 0001c000 08:02 43548681
> /lib64/ld-2.5.so
> 300f61d000-300f61e000 rwxp 0001d000 08:02 43548681
> /lib64/ld-2.5.so
> 300f80-300f94f000 r-xp  08:02 43548690
> /lib64/libc-2.5.so
> 300f94f000-300fb4f000 ---p 0014f000 08:02 43548690
> /lib64/libc-2.5.so
> 300fb4f000-300fb53000 r-xp 0014f000 08:02 43548690
> /lib64/libc-2.5.so
> 300fb53000-300fb54000 rwxp 00153000 08:02 43548690
> /lib64/libc-2.5.so
> 300fb54000-300fb59000 rwxp 300fb54000 00:00 0
> 300fc0-300fc82000 r-xp  08:02 43549057
> /lib64/libm-2.5.so
> 300fc82000-300fe81000 ---p 00082000 08:02 43549057
> /lib64/libm-2.5.so
> 300fe81000-300fe82000 r-xp 00081000 08:02 43549057
> /lib64/libm-2.5.so
> 300fe82000-300fe83000 rwxp 00082000 08:02 43549057
> /lib64/libm-2.5.so
> 301000-3010002000 r-xp  08:02 43548960
> /lib64/libdl-2.5.so
> 3010002000-3010202000 ---p 2000 08:02 43548960
> /lib64/libdl-2.5.so
> 3010202000-3010203000 r-xp 2000 08:02 43548960
> /lib64/libdl-2.5.so
> 3010203000-3010204000 rwxp 3000 08:02 43548960
> /lib64/libdl-2.5.so
> 301040-3010414000 r-xp  08:02 43548948
> /lib64/libz.so.1.2.3
> 3010414000-3010613000 ---p 00014000 08:02 43548948
> /lib64/libz.so.1.2.3
> 3010613000-3010614000 rwxp 00013000 08:02 43548948
> /lib64/libz.so.1.2.3
> 301080-3010816000 r-xp  08:02 43548875
> /lib64/libpthread-2.5.so
> 3010816000-3010a16000 ---p 00016000 08:02 43548875
> /lib64/libpthread-2.5.so
> 3010a16000-3010a17000 r-xp 00016000 08:02 43548875
> /lib64/libpthread-2.5.so
> 3010a17000-3010a18000 rwxp 00017000 08:02 43548875
> /lib64/libpthread-2.5.so
> 3010a18000-3010a1c000 rwxp 3010a18000 00:00 0
> 3018a0-3018b34000 r-xp  08:02 28578909
> /usr/lib64/libxml2.so.2.6.26
> 3018b34000-3018d34000 ---p 00134000 08:02 28578909
> /usr/lib64/libxml2.so.2.6.26
> 3018d34000-3018d3d000 rwxp 00134000 08:02 28578909
> /usr/lib64/libxml2.so.2.6.26
> 3018d3d000-3018d3e000 rwxp 3018d3d000 00:00 0
> 301da0-301da0d000 r-xp  08:02 43549037
> /lib64/libgcc_s-4.1.2-20080825.so.1
> 301da0d000-301dc0d000 ---p d000 08:02 43549037
> /lib64/libgcc_s-4.1.2-20080825.so.1
> 301dc0d000-301dc0e000 rwxp d000 08:02 43549037
> /lib64/libgcc_s-4.1.2-20080825.so.1
> 2b2d78bef000-2b2d78bf1000 rwxp 2b2d78bef000 00:00 0
> 2b2d78c0f000-2b2d78c1 rwxp 2b2d78c0f000 00:00 0
> 2b2d78c1-2b2d78c9e000 r-xp  00:1d 149134
> /rvol/cpse-apps/RHEL5-x86_64/gromacs-4.5.5/lib/libgmxpreprocess.so.6
> 2b2d78c9e000-2b2d78e9d000 ---p 0008e000 00:1d 149134
> /rvol/cpse-apps/RHEL5-x86_64/gromacs-4.5.5/lib/libgmxpreprocess.so.6
> 2b2d78e9d000-2b2d78e9f000 rwxp 0008d000 00:1d 149134
> /rvol/cpse-apps/RHEL5-x86_64/gromacs-4.5.5/lib/libgmxpreprocess.so.6
> 2b2d78e9f000-2b2d78ecb000 rwxp 2b2d78e9f000 00:00 0
> 2b2d78ecb000-2b2d7900b000 r-xp  00:1d 149131
> /rvol/cpse-apps/RHEL5-x86_64/gromacs-4.5.5/lib/libmd.so.6
> 2b2d7900b000-2b2d7920b000 ---p 0014 00:1d 149131
> /rvol/cpse-apps/RHEL5-x86

Re: [gmx-users] question

[jkrieger]

If you want Zn2+ ions to actually do something useful then rather than
just balance the charges you might want more of them - otherwise they
might just diffuse around. You could use the -conc flag with the -neutral
flag.

>
>
> On 12/5/13 6:10 AM, Andrew Bostick wrote:
>> Hi gmx users
>>
>> I am beginner in gromacs. Excuse me for my simple and ordinary
>> questions.
>> ---
>>
>> 1) In the most of tutorials and papers I read to now, for the simulation
>> of
>> a protein
>> with a net charge (for example: -5 e) in aqueous solution, counterions
>> (in this case: 5 Na ions) are added to neutralize the system. I have a
>> question about
>> that. Is neutralization of the system prior to md simulation mandatory
>> in
>> the gromacs?
>>
>
> Neutralization of a system is not decided based on the software, it is
> decided
> based on the algorithms used and what they require; that's true of any MD
> program.  The short answer is: it depends on what you are doing.  This
> topic has
> been discussed extensively on the mailing list, even in recent days.
> Google is
> your friend.
>
>> If I want to do md simulation of my protein in the presence of Zn2+
>> ions,
>> How to
>> manage both of (a) neutralize the system and (b) addition of specific
>> concentration
>> or number of Zn2+ ions (for example: 3 zinc ions) simultaneously?
>>
>> I know using [genion -s ions.tpr -o system.gro -p topol.top -np 5 -pname
>> NA
>> -pq +1]
>> is true for (a). But for (b), I have not opinion.
>
> If the ions are a necessary component of the system, that simply changes
> the net
> charge of the system.  If the protein is -5 e and the ions sum to +6 e,
> then
> your solute has a net charge of +1 e.  You can easily add the 3 Zn2+ and 1
> Cl-
> (or whatever else) counterion in one genion command.
>
>> ---
>>
>> 2) What is default value for pH in gromacs? Is pH of system during
>> simulation constant?
>
> There is no default pH.  Given that there are no exchangeable protons in a
> classical MD simulation, the protonation states of whatever molecules you
> have
> are chosen by you.  Titratable residues can be adjusted with relevant
> pdb2gmx
> command-line options.
>
>> Can I change pH value in mdp file? On the other hand, can I study 3 md
>> simulations with
>> 3 different pH (4.5, 7, 9.5)? I did not find issue about pH in chapter 7
>> of
>> the manual.
>>
>
> There is no .mdp option for this; it is a function of the topology and is
> set
> when running pdb2gmx.  You need to know the pKa values of all the
> titratable
> residues and set their protonation states accordingly.  One cannot really
> argue
> that you are doing a simulation at any pH value at all, but you are
> instead
> simulating the dominant species that would occur in a solution at that pH.
>
>> Does the protonation of the species present in the simulation determine
>> pH
>> of system?
>>
>
> Not according to the standard definition of what pH is.  There are no
> hydronium
> ions in the system, and even if there were, they can't behave in any
> realistic
> way in a classical simulation.
>
>> For example, if I have 3 lysine in my protein and N-terminal and
>> C-terminal
>> be NH3+ and
>> COO-, respectively, pH for my system will be 3?
>
> That would be a false statement.  Net charge and pH are not equivalent.
>
>> ---
>>
>> 3) In some pdb files, there are missing atoms or missing residues. If I
>> want to not use
>> -missing option of pdb2gmx and missing atoms or missing residues be very
>> important in my
>> study, is there a way to obtain this missing atoms or missing residues?
>
> There are many modeling programs and even some web servers that will
> rebuild
> missing atoms, residues, or loops.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> 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
>
> ==
> --
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Re: [gmx-users] Atomistic Simulation

[jkrieger]

You don't need to. Later processing steps such as editconf, genbox and
grompp can read .pdb files.

> so How do I convert from .pdb to .gro the ?
>
> --
> View this message in context:
> http://gromacs.5086.x6.nabble.com/Atomistic-Simulation-tp5012984p5013058.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
> --
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Re: [gmx-users] rcoulomb, rvdw and rlist values

[jkrieger]

The values of these cutoffs is specific to each forcefield - it's best not
to change them if you can't justify why. It doesn't say in the original
paper where they created parmbsc0 as far as I can tell but perhaps you can
find a later paper where they do say. Good luck.

> Dear Users
> I want to use parmbsc0 force field for DNA-ligand interaction. I want some
> information about value of rcoulomb, rvdw and rlist in mdp file during
> equilibration & production steps.
> I set these values 1 nm . Is it correct?
>
> Best regards
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Re: [gmx-users] double precision and minimisation error

[jkrieger]

As has been asked a number of times before, I have seen minimization halt
at a low number of steps having converged to machine precision when double
precision is not used - does that not mean that double precision is needed
at least for minimization? Sorry to ask this question again but I can't
find a clear answer to this in previous messages.

Many thanks
James

> You don't; you configure your MPI environment to have 8 ranks, which could
> be as simple as mpirun -np 8 mdrun_mpi.
>
> Generally you do not need double precision with GROMACS, unless you can
> say
> exactly why you need to trade away your simulation performance.
>
> Mark
> On Nov 29, 2013 9:15 PM, "Mahboobeh Eslami" 
> wrote:
>
>> i want to install gromacs4.6.3 on 8 core.
>> i use following command:
>>
>> CMAKE_PREFIX_PATH=/usr/local/openmpi/:/home/elahe/ComTools/fftw/ cmake
>> ..
>> -DGMX_MPI=ON -DGMX_THREAD_MPI=ON -DBUILD_SHARED_LIBS=OFF
>> -DGMX_PREFER_STATIC_LIBS=ON -DGMX_DOUBLE=ON
>> -DCMAKE_INSTALL_PREFIX=/home/elahe/ComTools/gromacs
>> is it correct?
>> What command do I use to use 8 cores? which valid command line argument
>> do
>> i use by mdrun_mpi_d for 8 cores.
>> thanks a lot
>> --
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Re: [gmx-users] Mailing list archive

[jkrieger]

There was a message that the server would be down from midnight to 18:00 GMT+1

On 26 Nov 2013, at 21:08, "Andrew DeYoung"  wrote:

> Hi,
> 
> Does anyone know if the gmx-users Archive has been moved or is temporarily
> down?  When I do to:
> 
> http://lists.gromacs.org/pipermail/gmx-users/
> 
> it redirects me to:
> 
> https://mailman-1.sys.kth.se/pipermail/gmx-users/
> 
> but that page says, "The requested URL /pipermail/gmx-users/ was not found
> on this server."
> 
> Thanks!
> 
> Andrew DeYoung
> Carnegie Mellon University
> 
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Re: [gmx-users] Invalid order for directive bondtypes

[jkrieger]

You can't send attachments to the list. Please upload it somewhere (eg Dropbox) 
and include a link.

On 26 Nov 2013, at 08:39, Elham Gholamrezai  wrote:

> 
> 
> 
> 
> 
> 
> 
> Dear all
> 
> I am working on simulation of hydrogen adsorption on graphene sheet, and I 
> need to adopte my force field parameters, new force field folder is made and 
> put in top directory of gromacs. For this reason, I modified "charmm27.ff" 
> and included new files (bond.itp, nonbond.itp, n2t, atp, rtp, force 
> field.itp) in it first, then topology file was produced by g_x2top command 
> without any error. But when I grompp for minimization, I got the following 
> error. How can I solve it? I used this command for grompp 
> 
> grompp -f em.mdp -c conf.gro -p topol.top -o em.tpr -n index.ndx
> 
> (also conf.gro include hydrogen and graphene sheet)
>  
> 
> Fatal error:
> Syntax error - File ffbonded.itp, line 1
> Last line read:
> '[ bondtypes ]'
> Invalid order for directive bondtypes
> 
> I also attach ffbonded.itp file.
> 
>  any help is appreciated.
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Re: [gmx-users] problems with chain IDs for huge complex

[jkrieger]

Maybe the answer is to not worry about chain identifiers until analysis
stages - you could probably just call everything chain A at the start. You
can then create an index entry for each chain. See
http://www.gromacs.org/Documentation/How-tos/Multiple_Chains

> As far as I remember in pdb format you can only use one character for
> chain
> id.
>
>
>
> On Mon, Nov 18, 2013 at 7:05 PM,  wrote:
>
>> How about naming your chains AA-AZ then BA-BZ? You probably need to
>> change
>> the chain names in the original structures rather than just renaming the
>> files.
>>
>> > Hi,
>> >
>> > I am preparing simulation of the ribosome and because of it size I am
>> > force
>> > to use A-Z and a-z to name all chains...
>> > With pdb2gmx it is not a problem but with grompp I am ending up with
>> this
>> > error (gromacs 4.6.3):
>> >
>> > Fatal error:
>> > moleculetype Protein_chain_b is redefined
>> >
>> > I figured out that for grompp Protein_chain_b and Protein_chain_B are
>> the
>> > same entry - and hence error...
>> > I changed the name of files in this fashion:
>> > Protein_chain_b -> Protein_chain_bb etc
>> > And now grompp was able to read them but it found out that there is
>> > different number of atoms between top and gro file..
>> > Any ideas or suggestions?
>> > Thanks.
>> > Best
>> >
>> > tomek
>> > --
>> > gromacs.org_gmx-users mailing list
>> > gromacs.org_gmx-users@maillist.sys.kth.se
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>> >
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>>
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Re: [gmx-users] problems with chain IDs for huge complex

[jkrieger]

How about naming your chains AA-AZ then BA-BZ? You probably need to change
the chain names in the original structures rather than just renaming the
files.

> Hi,
>
> I am preparing simulation of the ribosome and because of it size I am
> force
> to use A-Z and a-z to name all chains...
> With pdb2gmx it is not a problem but with grompp I am ending up with this
> error (gromacs 4.6.3):
>
> Fatal error:
> moleculetype Protein_chain_b is redefined
>
> I figured out that for grompp Protein_chain_b and Protein_chain_B are the
> same entry - and hence error...
> I changed the name of files in this fashion:
> Protein_chain_b -> Protein_chain_bb etc
> And now grompp was able to read them but it found out that there is
> different number of atoms between top and gro file..
> Any ideas or suggestions?
> Thanks.
> Best
>
> tomek
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Re: [gmx-users] a query

[jkrieger]

Try sending your problem in the same way you sent this email. They should
be the same.

Maybe it hadn't processed your subscription at the time you sent your
problem and now it will work.

>
>
> i have posted a problem in gronacs user forum ...but its saying that it
> is not accepted by the mailing list yet..
>
> althuogh i am already a subscriber to it..
>
> please suggest
>
> --
> VANDNA
> JRF
> C/O Dr. Girish Sahni
> Protein Science lab
> Phone No. 0172-2690830
> Institurte of Microbial Technology (IMTech)
> Sector -39A, Chandigarh,160036
>
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Re: [gmx-users] GROMACS 4.6.4 is released

[jkrieger]

Thanks Mark.

On 14 Nov 2013, at 10:20, Mark Abraham  wrote:

> Hi,
> 
> Good question. That is our hope, from the way we have selected and
> implemented the changes in 4.6.x series. Except actual bug fixes, of
> course! The idea is that the new patch release implements the same physics,
> so a restart should be seamless. You can take any 4.6.x and restart it on a
> different number of processors and there should be no observable change
> apart from mdrun warning you that reproducibility is now even more
> impossible. Restarting with a later 4.6.x should work similarly smoothly.
> 
> However, it's completely infeasible for us to test all the possibilities,
> even had we the resources to attempt it. So, I would strongly encourage you
> to test that you can observe no problems before you commit to that
> strategy. As a reviewer, I would expect that you showed that changing your
> black-box method was not a change of method. Throwing away a few
> nanoseconds after the restart should be ample relaxation, if any were
> required.
> 
> Mark
> On Nov 13, 2013 6:31 PM,  wrote:
> 
>> Will a simulation from 4.6.1 continue running fine if I upgrade to 4.6.4?
>> 
>>> Hi GROMACS users,
>>> 
>>> GROMACS 4.6.4 is officially released. It contains numerous bug fixes, and
>>> some noteworthy simulation performance enhancements (particularly with
>>> GPUs!). We encourage all users to upgrade their installations from
>> earlier
>>> 4.6-era releases.
>>> 
>>> You can find the code, manual, release notes, installation instructions
>>> and
>>> test
>>> suite at the links below. Note that some tests have been added, and the
>>> manual has changed only in chapter 7 and appendix D.
>>> 
>>> ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.4.tar.gz
>>> ftp://ftp.gromacs.org/pub/manual/manual-4.6.4.pdf
>> http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.6.x#Release_notes_for_4.6.4
>>> http://www.gromacs.org/Documentation/Installation_Instructions
>>> http://gromacs.googlecode.com/files/regressiontests-4.6.4.tar.gz
>>> 
>>> Happy simulating!
>>> 
>>> The GROMACS team
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>> 
>> 
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