Re: [gmx-users] restart failed

2013-11-18 Thread Mark Abraham
On Sat, Nov 16, 2013 at 10:46 AM, xiao helitr...@126.com wrote: Hi all gromacs users, My simulation crashed, and i try to restart it by using the following command: mdrun -s topol.tpr -cpi state.cpt Not using -deffnm means mdrun expects to write traj.trr, traj.xtc, ener.edr... The

Re: [gmx-users] installing latest version of gromacs 4.6.3

2013-11-18 Thread Mark Abraham
Your system is configured such that it recognizes the (old) version of GROMACS you could get with the command it lists. Since you want the latest version (which is no longer 4.6.3!) do what you've done and make sure you finish reading

Re: [gmx-users] nstlist and performances

2013-11-19 Thread Mark Abraham
charge groups and defaults with a buffer. ;-) Mark On Mon, Nov 18, 2013 at 9:50 PM, Mark Abraham mark.j.abra...@gmail.com wrote: On Mon, Nov 18, 2013 at 3:58 PM, Riccardo Concu ric.co...@gmail.com wrote: Dear all, I'm running a simulation of a quite big system and is running very

Re: [gmx-users] installing latest version of gromacs 4.6.3

2013-11-19 Thread Mark Abraham
Google knows a lot more about generic UNIX non-GROMACS tasks like configuring your shell than we do ;-) Mark On Tue, Nov 19, 2013 at 5:08 AM, vansh vsha...@imtech.res.in wrote: can you please suggest me how to get this ..i am using bash shell - thanks in advance :) -- View this

Re: [gmx-users] nstlist and performances

2013-11-19 Thread Mark Abraham
any code doing anything unbuffered. Whether the force field can live up to that on a given system is unknown until it is observed. Mark Thanks, On Tue, Nov 19, 2013 at 4:52 PM, Mark Abraham mark.j.abra...@gmail.com wrote: On Tue, Nov 19, 2013 at 6:12 AM, rajat desikan rajatdesi

Re: [gmx-users] Expanding of the boundaries of the enssemble

2013-11-20 Thread Mark Abraham
Take a frame, apply editconf and genbox? Mark On Nov 20, 2013 6:40 AM, James Starlight jmsstarli...@gmail.com wrote: Dear Gromacs Users, I have 10 snapshots of the MD trajectory in dcd format. Presently I'd like to expand boundaries of my system (in all of that 10 conformers) in Z dimension

Re: [gmx-users] Invalid order for directive bondtypes

2013-11-26 Thread Mark Abraham
You're including that file from somewhere that violates the rules in chapter 5. But only you know where. Mark On Nov 26, 2013 11:07 AM, Elham Gholamrezai elham.gholamre...@yahoo.com wrote: Dear all I am working on simulation of hydrogen adsorption on graphene sheet, and I need to adopte my

Re: [gmx-users] energy group tables

2013-11-26 Thread Mark Abraham
Try it! You surely have a test run that will show that your tables work, before you launch into production work, right? :-) On Nov 26, 2013 5:16 AM, Chandan Choudhury iitd...@gmail.com wrote: On Mon, Nov 25, 2013 at 11:22 PM, Humberto Saint-Martin xibas...@gmail.comwrote: Hi, Chandan,

Re: [gmx-users] Coulombic potential modifiers in Gromacs 4.6.4.

2013-11-26 Thread Mark Abraham
? Not at all ;-) Mark Thanks, I appreciate your time. The manual did not have the answers I need. On Fri, Nov 22, 2013 at 10:03 PM, Mark Abraham mark.j.abra...@gmail.com wrote: On Nov 21, 2013 9:20 AM, rajat desikan rajatdesi...@gmail.com wrote: Hi All, I was wondering about

[gmx-users] planned power outage

2013-11-26 Thread Mark Abraham
Hi GROMACS users and devs, There's a planned power outage tomorrow (November 27) to the machine room that houses most of the GROMACS infrastructure. This will mean a period of unavailability of everything except the FTP server and perhaps the mailing lists. We expect no problems, and will bring

Re: [gmx-users] The 20 subsystems are not compatible (REMD)

2013-11-26 Thread Mark Abraham
On Tue, Nov 26, 2013 at 2:53 PM, Pacho Ramos pachora...@gmail.com wrote: Hello I am having a lot of problems to get a REMD simulation end, after running for some time, some replicas are interrupted without writting a state file, leading then to: The 20 subsystems are not compatible error

Re: [gmx-users] the changing of velocity in production stage

2013-11-26 Thread Mark Abraham
your stated objective. continuation = whatever is fine, given that you are equilibrating again. Mark Thank you very much On Tuesday, November 26, 2013 2:56 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Those are fine. I would equilibrate, then fork to do the generation, and do

Re: [gmx-users] # of threads different than # of cores - gmx hangs.

2013-11-26 Thread Mark Abraham
is not a multiple of the number of nodes. XAvier. On Nov 22, 2013, at 7:14 PM, XAvier Periole x.peri...@rug.nl wrote: Ok, tks. I'll try then :)) XAvier. On Nov 22, 2013, at 4:31 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Hardware detection and management of the results

Re: [gmx-users] calculate velocity autocorrelation function

2013-11-27 Thread Mark Abraham
Yes, per g_velacc -h ;-) Mark On Wed, Nov 27, 2013 at 2:54 PM, Mahboobeh Eslami mahboobeh.esl...@yahoo.com wrote: dear justin Do I need a special option in the mdp file. thanks a lot On Wednesday, November 27, 2013 4:40 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/27/13

Re: [gmx-users] step 0Segmentation fault: 11

2013-11-27 Thread Mark Abraham
Start with the simplest relevant system (e.g. two atoms with no bond). Then two atoms with bond. Then more complex. Now you have a chance of seeing what is wrong - particularly if there might be multiple things wrong! Mark On Wed, Nov 27, 2013 at 4:29 PM, Valentina

Re: [gmx-users] planned power outage

2013-11-27 Thread Mark Abraham
Hi all, Thanks for your patience. The planned power outage is now complete. GROMACS infrastructure is back online and working (but working out whether we can refine the mailing list implementation is ongoing). Mark On Tue, Nov 26, 2013 at 2:31 PM, Mark Abraham mark.j.abra...@gmail.comwrote

Re: [gmx-users] topology for small peptide using amber03

2013-11-28 Thread Mark Abraham
PDB format has fixed column widths. You cannot edit it correctly unless you preserve the layout - e.g. replace deleted characters with spaces. Mark On Nov 28, 2013 4:26 AM, kolnkempff kolnkem...@gmail.com wrote: /I am trying to use pdb2gmx to get a topology for a very simple peptide that has

Re: [gmx-users] step 0Segmentation fault: 11

2013-11-28 Thread Mark Abraham
Huge forces lead to crazy displacements whose next forces are looked up outside the boundaries of your table, which leads to a segmentation fault. GROMACS doesn't waste its time checking for this, since that would hurt everyone's performance and gain only a descriptive error that something is

Re: [gmx-users] REMD on GPU

2013-11-28 Thread Mark Abraham
On Thu, Nov 28, 2013 at 3:01 PM, James Starlight jmsstarli...@gmail.comwrote: Dear Gromacs users! I'd like to perform replica exchange simulation For this I've made bash script which create n folders like replica-298 replica-312 replica-323 replica-334 ... replica-N with all files

Re: [gmx-users] valid command line argument do i use by mdrun_mpi_d for 8 cores.

2013-11-29 Thread Mark Abraham
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

Re: [gmx-users] Charge correction PME

2013-11-30 Thread Mark Abraham
... but not necessarily any good! See https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-developers/2012-November/006398.html. I have seen Gerrit present some convincing results since then, but they do not seem to be in press, yet. Neutralizing explicitly seems like the right course just

Re: [gmx-users] ATB SERVER

2013-12-01 Thread Mark Abraham
There are probably a few tutorials that describe what you're trying to do. Probably none of them are exactly right, but you will learn from doing them regardless. Please do a preliminary search for information before asking questions! :-) Mark On Dec 1, 2013 10:38 PM, Mahboobeh Eslami

Re: [gmx-users] using nopbc is not equal to using pbc with big box dimensions

2013-12-02 Thread Mark Abraham
Hi, We could guess, or maybe you could share what was in your two .mdp files and how they differ ;-) E.g. report the diff here and upload the originals to an online file-sharing service and link them. Mark On Mon, Dec 2, 2013 at 11:46 PM, Golshan Hejazi golshan.hej...@yahoo.comwrote: Hello,

Re: [gmx-users] What does it mean that particle decomposition does not support checkpointing?

2013-12-09 Thread Mark Abraham
Hi, Sorry, I don't remember the observation that led to my statement, but I believed it to be true and since pretty much none of the developers still use particle decomposition, nobody has corrected me! Your observations suggest that checkpointing is working fine for you. You should be able to

Re: [gmx-users] pressure based replica exchange

2013-12-10 Thread Mark Abraham
On Tue, Dec 10, 2013 at 1:47 PM, Jianguo Li ljg...@yahoo.com.sg wrote: Dear All, Is it possible to do pressure based replica exchange simulations in gromacs? Basically I want to do replica exchange simulations for my membrane system at different surface tensions. If I just set different

Re: [gmx-users] Normal Mode Analysis with Gromacs 4.6

2013-12-12 Thread Mark Abraham
Why are you using PME-switch? Without explicitly choosing a switch? Mark On Thu, Dec 12, 2013 at 6:45 PM, mcfc1301 mcfc1...@gmail.com wrote: Hello Everyone, I'm confused about Normal Mode Analysis of Gromacs. I have googled a lot but find little useful. My Gromacs was installed in a

Re: [gmx-users] pressure based replica exchange

2013-12-12 Thread Mark Abraham
). But there is no pressure term in the acceptance criteria (eq 3.143). I am wondering if pressure+temperature+Hamiltonian replica exchange has been implemented in Gromacs. If yes, what is the general equation of acceptance criteria? Cheers, Jianguo On Tuesday, 10 December 2013, 17:49, Mark

Re: [gmx-users] Fw: Error in extendig md run in gromacs

2013-12-13 Thread Mark Abraham
No, GROMACS is reporting that the conditions that produced the supplied checkpoint are different from those of the current mdrun. This is not a problem - you could have done the equivalent of first run with the conditions of the second, after all - but GROMACS noting the event is perhaps useful

Re: [gmx-users] Gromos DPPC bilayer: different results for 4.0.7 and 4.6.5

2013-12-17 Thread Mark Abraham
On Wed, Dec 18, 2013 at 6:58 AM, Lutz Maibaum lutz.maib...@gmail.comwrote: 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

Re: [gmx-users] conversion of X,Y,Z + velocities to *.trr

2013-12-22 Thread Mark Abraham
Hi, Constructing a .tpr is covered many GROMACS tutorials you can find. What is particular about your case that you do not have one from doing the simulation? Mark On Mon, Dec 23, 2013 at 9:40 AM, Rasoul Nasiri nasiri1...@gmail.com wrote: Many thanks Tsjerk, Let me ask another question. As

Re: [gmx-users] hanging regression test with MPI-enabled GROMACS v4.6.1 or v4.6.5 (GCC/OpenMPI/OpenBLAS/FFTW)

2013-12-22 Thread Mark Abraham
Hi, Thanks for the report. For diagnosis, I would suggest using the GROMACS internal BLAS and LAPACK, since those you are supplying seem like they might have OpenMP support. Such support would be likely not useful for GROMACS, and is perhaps a contributor to this problem. Accordingly, don't do

Re: [gmx-users] conversion of X,Y,Z + velocities to *.trr

2013-12-23 Thread Mark Abraham
and/or reference coordinates, a .gro/.pdb file will do. Only if you need to have bonds/masses/charges/... you really need a .tpr file for reference. Cheers, Tsjerk On Mon, Dec 23, 2013 at 4:00 AM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, Constructing a .tpr is covered

Re: [gmx-users] error on running job in parallel

2014-01-01 Thread Mark Abraham
Hi, It's not a GROMACS error, so you'll have to solve that one yourself. Leading suspect is that the above example does not work with that mpirun, because mpirun is trying to interpret -s (and giving an error) rather than passing the argument to mdrun. See the mpirun docs and talk more to the

Re: [gmx-users] simulation using tabulated dihedral potentials.

2014-01-05 Thread Mark Abraham
On Sun, Jan 5, 2014 at 5:51 AM, Chandan Choudhury iitd...@gmail.com wrote: On Sat, Dec 28, 2013 at 5:24 AM, Justin Lemkul jalem...@vt.edu wrote: On 12/27/13, 12:58 AM, Chandan Choudhury wrote: Dear Justin and Mark, Thanks for the reply. I have regenerated the potentials for the

Re: [gmx-users] Overriding Wildcard dihedraltypes

2014-01-09 Thread Mark Abraham
Hi, Thanks for the question, and particularly the detail. It seems that you are trying use a [dihedraltypes] section in my_molecule.itp, which is generally a bad idea, because all such directives must appear before the first [molecule] directive, which defeats the point of molecule.itp files

Re: [gmx-users] Reg Replica exchange Molecular dynamics

2014-01-14 Thread Mark Abraham
Google knows about two GROMACS REMD tutorials, by the way! Mark On Tue, Jan 14, 2014 at 1:30 PM, vidhya sankar scvsankar_...@yahoo.comwrote: Dear Justin Thank you For your previous reply I would like to do REMD (Replica exchange MD) in gromacs I am very happy if you paste tutorial for

Re: [gmx-users] how to modify the shake algorithm

2014-01-14 Thread Mark Abraham
I'd imagine using constraint type 2 between suitable virtual sites would be a much better approach. Not sure it actually works, though! Mark On Tue, Jan 14, 2014 at 8:01 PM, Yuan Hu neofl...@gmail.com wrote: Dear Gromacs user/developer, I want to modify the Shake program in gromacs 4.x to

Re: [gmx-users] scale tabulated non-bonded potentials?

2014-01-15 Thread Mark Abraham
Yes, they get multiplied by parameters like charge, C6, C12 etc. Is that the question you're asking? :-) Mark On Wed, Jan 15, 2014 at 8:02 PM, Steven Neumann s.neuman...@gmail.comwrote: Dear Gmx Users, Is there any way in Gromacs to scale tabulated potentials from energygrp_table

Re: [gmx-users] g_helix segmentation fault grom-4.6.5

2014-01-15 Thread Mark Abraham
Software has bugs, unfortunately, and GROMACS tools particularly so. We are trying to improve the situation, but if a developer isn't using a tool, it doesn't get any love! Are you trying to say it doesn't work in 4.6.5? Mark On Jan 16, 2014 5:51 AM, tarak karmakar tarak20...@gmail.com wrote:

Re: [gmx-users] gromacs bond restraints

2014-01-15 Thread Mark Abraham
See chapter four for what is available, and tables in 5.5 for a summary of their use. Mark On Jan 16, 2014 5:11 AM, Neha Gandhi n.gandh...@gmail.com wrote: How can I impose restraints in gromacs .mdp file or topology file to avoid isomerization of the peptide bond at the highest temperatures?

Re: [gmx-users] scale tabulated non-bonded potentials?

2014-01-16 Thread Mark Abraham
two non-zero columns - potential and its derivative present. How can I I scale it by 0.5 for example? Steven On Wed, Jan 15, 2014 at 10:30 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Yes, they get multiplied by parameters like charge, C6, C12 etc. Is that the question you're

Re: [gmx-users] choose the reference structure of Gromacs

2014-01-18 Thread Mark Abraham
Hi, See g_rms -h first ;-) Mark On Sat, Jan 18, 2014 at 3:17 PM, Ahmet yıldırım ahmedo...@gmail.com wrote: Dear users, How do Gromacs choose the reference structure for the fit the trajectory? For example: g_rms -f traj.xtc -s topol.tpr The reference structure is first frame (-dump

Re: [gmx-users] Installing Gromacs 4.6.5 - Problem with FFTW

2014-01-18 Thread Mark Abraham
Hi, I am trying to install Gromacs 4.6.5 on Kubuntu. My Kubuntu skills are not that good, so I kept close to the Install Instructions. I skipted the Quick and Dirty Instrucitons and now I should be at the point 4.1 Configuring with CMake. When I insert cmake .., I recieve: Can anyone tell

Re: [gmx-users] Vacuum disappear after NPT equilibration?

2014-01-18 Thread Mark Abraham
of Mark Abraham mark.j.abra...@gmail.com Sent: Saturday, January 18, 2014 5:21 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Vacuum disappear after NPT equilibration? Hi, Why are you trying to maintain a region of vacuum while changing the density of the rest? Mark

Re: [gmx-users] future of shell completions in GROMACS

2014-01-20 Thread Mark Abraham
Hi, Also, current developer discussion can be found here http://redmine.gromacs.org/issues/1410, and experience and input even for bash is welcome! Mark On Mon, Jan 20, 2014 at 3:01 PM, Mark Abraham mark.j.abra...@gmail.comwrote: Hi, Past versions of GROMACS supported source-ing completion

[gmx-users] future of shell completions in GROMACS

2014-01-20 Thread Mark Abraham
Hi, Past versions of GROMACS supported source-ing completion.* shell files from the installation directory, so that you could do things like grompp -f myinp followed by a tab keypress to do UNIX-style command completion that would correctly work out that myinputfile.mdp was an appropriate

Re: [gmx-users] Installing Gromacs 4.6.5 - Problem with FFTW

2014-01-20 Thread Mark Abraham
the required installation for FFTW3 but still this error occcurs. If I get you right, then I can proceed with the install and everything will be fine? Marvin Am 18.01.2014 18:28, schrieb Mark Abraham: Hi, I am trying to install Gromacs 4.6.5 on Kubuntu. My Kubuntu skills are not that good

Re: [gmx-users] grompp erro

2014-01-21 Thread Mark Abraham
My question related to your choice at the N terminus. Your existing atoms seem to be a methylated amine, which you probably should not want to change. Mark On Jan 21, 2014 9:17 AM, Albert mailmd2...@gmail.com wrote: On 01/21/2014 12:46 AM, Mark Abraham wrote: Why are you trying to make

Re: [gmx-users] Maximal nrexcl

2014-01-21 Thread Mark Abraham
Or use rerun with each pair of molecules alone, by constructing a large number of sets of matching input subsets from using tpbconv and trjconv. Mark On Jan 21, 2014 4:54 AM, Justin Lemkul jalem...@vt.edu wrote: On 1/20/14, 8:17 PM, cynthiahong1983 wrote: Dear All, Does anyone know

Re: [gmx-users] Rerun error

2014-01-24 Thread Mark Abraham
What does gmxcheck say about this files? Mark On Fri, Jan 24, 2014 at 3:49 PM, Shima Arasteh shima_arasteh2...@yahoo.comwrote: Hi, I had a large .trr file, tried to do rerun on it. First I used split command and made 10 new .trr files with 2G in size. Then ran rerun on the first 2G.trr,

Re: [gmx-users] reseed

2014-01-24 Thread Mark Abraham
No, see gen-vel in .mdp settings. Mark On Fri, Jan 24, 2014 at 3:30 PM, Jacopo Sgrignani sgri...@gmail.com wrote: Dear all I would like to run multiple independent simulations reassigning starting velocities, does the -reseed option work only in REMD or also for standard MD? thanks

Re: [gmx-users] Rerun error

2014-01-24 Thread Mark Abraham
0 Sincerely, Shima From: Mark Abraham mark.j.abra...@gmail.com To: Discussion list for GROMACS users gmx-us...@gromacs.org; Shima Arasteh shima_arasteh2...@yahoo.com Sent: Friday, January 24, 2014 6:43 PM Subject: Re: [gmx-users] Rerun

Re: [gmx-users] Rerun error

2014-01-26 Thread Mark Abraham
, Mark Abraham mark.j.abra...@gmail.com wrote: You're using unix split? That could work for .trr under the right conditions, but apparently it is not. trjconv has a million different ways to split trajectories, so try them. Also chekc that your file system can handle files bigger than

Re: [gmx-users] Adding Ions step

2014-01-26 Thread Mark Abraham
On Jan 26, 2014 10:57 AM, Mahboobeh Eslami mahboobeh.esl...@yahoo.com wrote: hi GMX users The output of pdb2gmx told me that the protein-ligand complex has a net charge of 0(zero) but at the last line of my[ atoms ] directive in topol.top;qtot 2.749e-06 . be read . 1)What does this mean?

Re: [gmx-users] center of dodecahedron

2014-01-26 Thread Mark Abraham
On Jan 26, 2014 9:30 AM, Mahboobeh Eslami mahboobeh.esl...@yahoo.com wrote: hi GMX users i simulate protein ligand complex in dodecahedron box when i use following command editconf -f complex.pdb -o newbox.gro -bt dodecahedron -d 1.0 -c My complex is not located in the center of box, How

Re: [gmx-users] can we differentiate it?

2014-01-27 Thread Mark Abraham
No, but genion asks you for a group of solvent molecules to use as the candidates for replacement. You wish to differentiate two different sub-groups, which you can do in advance in your genion -n file, e.g. generated using a geometric criterion in g_select. This kind of Unix-style re-use is why

Re: [gmx-users] Rerun error

2014-01-27 Thread Mark Abraham
to a cluster or a more powerful system? Sincerely, Shima On Sunday, January 26, 2014 11:50 AM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, Thanks for the full description. It seems like your file system cannot handle files over 2gb even for splitting, which is not surprising, because

Re: [gmx-users] job error in cluster

2014-01-28 Thread Mark Abraham
That's extremely strange. There's a bug there to fix (48 cannot be correct in both places it is used). Albert, can you please upload your .tpr to a new issue at http://redmine.gromacs.org? Please also add what value of OMP_NUM_THREADS is set (perhaps implicitly by the script or your mpirun or

Re: [gmx-users] At what point is the random seed generated?

2014-01-28 Thread Mark Abraham
Indeed. grompp does report the seed it uses to stderr. Mark On Tue, Jan 28, 2014 at 8:51 AM, David van der Spoel sp...@xray.bmc.uu.sewrote: On 2014-01-28 08:37, Trayder Thomas wrote: Hi, When using 'gen-seed = -1' at what point is the random seed assigned? e.g. Does it use the process ID

Re: [gmx-users] how can I exclude the solvent from the output?

2014-01-28 Thread Mark Abraham
Hi, That doesn't apply to an energy minimization, which rarely writes enough output to care about at all. xtc-grps are active for the other kinds of integrators in mdrun. Mark On Tue, Jan 28, 2014 at 6:13 PM, Athina Meletiou enxa...@nottingham.ac.ukwrote: Hello! I am interested in running

Re: [gmx-users] Supported features in Gromacs on GPU

2014-01-28 Thread Mark Abraham
On Tue, Jan 28, 2014 at 10:26 PM, Andrew DeYoung adeyo...@andrew.cmu.eduwrote: Hi, It seems that Gromacs support for GPU began with OpenMM (which works with Gromacs 4.5). But starting with Gromacs 4.6, GPU support was native. I am interested in which features are currently implemented for

[gmx-users] GROMACS 5.0 - second beta released!

2014-01-29 Thread Mark Abraham
Hi GROMACS users, The second beta release of GROMACS 5.0 is available! We are making this available to you to get an early taste of how GROMACS 5.0 will look and work, and most importantly to get feedback from you about how well things work. While we try our hardest to keep the quality of GROMACS

Re: [gmx-users] At what point is the random seed generated?

2014-01-29 Thread Mark Abraham
! :-( Mark Oh well, Thanks guys. -Trayder On Tue, Jan 28, 2014 at 10:55 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Indeed. grompp does report the seed it uses to stderr. Mark On Tue, Jan 28, 2014 at 8:51 AM, David van der Spoel sp...@xray.bmc.uu.sewrote: On 2014-01-28

Re: [gmx-users] GROMACS 5.0 - second beta released!

2014-01-29 Thread Mark Abraham
Thanks. It'd be nice if MSVC did what it claims to do, and create more pages on demand for such allocations. Mark On Wed, Jan 29, 2014 at 6:59 PM, Mirco Wahab mirco.wa...@chemie.tu-freiberg.de wrote: On 29.01.2014 15:06, Mirco Wahab wrote: A test run (martini small vesicle system, 250K

Re: [gmx-users] Supported features in Gromacs on GPU

2014-01-30 Thread Mark Abraham
These are all standard in 4.6. The GPU implementation there only does non-bonded pair interactions, which affects none of the above. The limitation in 4.5 was that the GPU did lots more parts of the computation, and not all kinds of algorithms are amenable to that. Mark On Wed, Jan 29, 2014 at

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

2014-01-30 Thread Mark Abraham
On Jan 30, 2014 11:57 PM, Raffaella D'Auria rdau...@ucla.edu 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

Re: [gmx-users] codes for non-bonded function selection (NBF)

2014-02-02 Thread Mark Abraham
Hi, As you can see in the comment at the top of that file, you will need to make matching changes to some arrays in src/gmxlib/names.c Mark On Sat, Feb 1, 2014 at 3:11 AM, Makoto Yoneya makoto-yon...@aist.go.jpwrote: Dear Gromacs exparts: I'd like to add the non-boded function selection

Re: [gmx-users] Bond interaction exclusions

2014-02-02 Thread Mark Abraham
On Sun, Feb 2, 2014 at 5:29 PM, Xu Dong Huang xudonghm...@gmail.com wrote: Dear all, I am unclear about the bond exclusion properties within gromacs. Using a martini model system, what is the default behavior of setting [moleculetype] ;name exclusions eth 1 exclusions to 1? The

Re: [gmx-users] simulating multiple molecules in a box

2014-02-02 Thread Mark Abraham
On Sun, Feb 2, 2014 at 8:28 PM, ibrahim khalil ibrahim.khalil.c...@gmail.com wrote: hi, i am new to gromacs. i was trying simulate multiple (eg. 3 or 4 ) carbon nanotubes in a single box. The way I am trying to do is ... 1. Take both pdb files, merge them(using pymol) according to my

Re: [gmx-users] Simulating spherocylinders

2014-02-02 Thread Mark Abraham
No. Mark On Sun, Feb 2, 2014 at 7:25 PM, Sanku M msank...@yahoo.com wrote: Dear Gromacs users Is it possible to simulate md of rigid spherocylinders in grimaces? Thanks Sanku -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] leapfrog does not yet support Nose-Hoover chains

2014-02-03 Thread Mark Abraham
Hi, Protein chains and NH chains are entirely different things (see manual for latter). Probably for ligand-protein simulations the difference between NH with 1 chain and more is marginal, and probably smaller than your sampling error. You could a) use md-vv to get NH chains (but slower when run

Re: [gmx-users] multiple GPU on multiple nodes

2014-02-03 Thread Mark Abraham
On Tue, Feb 4, 2014 at 1:51 AM, cyberjhon cyberj...@hotmail.com wrote: Dear Szilárd Thanks for your answer. To submit the job I do; qsub -l nodes=2:ppn=16,walltime=12:00:00 Then, to run gromacs I can do: aprun -n 1 mdrun_mpi -deffnm protein And, I get the message that you mention,

Re: [gmx-users] multiple GPU on multiple nodes

2014-02-04 Thread Mark Abraham
OK, thanks! :-) Mark On Tue, Feb 4, 2014 at 12:20 PM, Szilárd Páll pall.szil...@gmail.comwrote: On Tue, Feb 4, 2014 at 2:31 AM, Mark Abraham mark.j.abra...@gmail.com wrote: On Tue, Feb 4, 2014 at 1:51 AM, cyberjhon cyberj...@hotmail.com wrote: Dear Szilárd Thanks for your answer

Re: [gmx-users] question about gromacs

2014-02-04 Thread Mark Abraham
Hi, As genrestr -h warns, you need a position restraint files per moleculetype, not for the whole set of such molecules. Mark On Tue, Feb 4, 2014 at 2:39 PM, Andrew Bostick andrew.bosti...@gmail.comwrote: Hi all My system contain dopc + cholesterol + water + drug molecules. I want to do

Re: [gmx-users] Custom urea topology

2014-02-05 Thread Mark Abraham
[moleculetype] UREA 1 looked odd. Why do you only want to exclude singly bonded neighbours from being nonbonded interactions? Mark On Wed, Feb 5, 2014 at 4:18 PM, Justin Lemkul jalem...@vt.edu wrote: On 2/5/14, 12:11 AM, Gabriele Lanaro wrote: I attached them but I think they didn't pass

Re: [gmx-users] There is no domain decomposition for nodes that is compatible

2014-02-05 Thread Mark Abraham
Depends on the size of your system and how much parallelism you want to use. See manual section on DD. Mark On Wed, Feb 5, 2014 at 4:58 PM, Steven Neumann s.neuman...@gmail.comwrote: Thank you. Can you specify what does long mean? Is there any limit? On Wed, Feb 5, 2014 at 3:49 PM, Justin

Re: [gmx-users] Different optimal pme grid ... coulomb cutoff values from identical input files

2014-02-05 Thread Mark Abraham
What's the network? If it's some kind of switched Infiniband shared with other user's jobs, then getting hit by the traffic does happen. You can see that the individual timings of the things the load balancer tries differ a lot between runs. So there must be an extrinsic factor (if the .tpr is

Re: [gmx-users] Different optimal pme grid ... coulomb cutoff values from identical input files

2014-02-06 Thread Mark Abraham
On Feb 6, 2014 8:42 AM, yunshi11 . yunsh...@gmail.com wrote: On Wed, Feb 5, 2014 at 9:43 AM, Mark Abraham mark.j.abra...@gmail.com wrote: What's the network? If it's some kind of switched Infiniband shared with other user's jobs, then getting hit by the traffic does happen. You can see

Re: [gmx-users] Simulations with Nitroxide Spin Label

2014-02-06 Thread Mark Abraham
On Feb 6, 2014 4:41 PM, akk5r ak...@virginia.edu wrote: Hi, Does anyone know if there is a way to incorporate a nitroxide spin labels into a gromacs simulation of proteins in water. With NMR and EPR it is possible to obtain distance restraints between labels, and I am interested to

Re: [gmx-users] g_cluster

2014-02-09 Thread Mark Abraham
Let's make sure we keep it friendly and constructive! :-) Mark On Feb 9, 2014 12:23 PM, João Henriques joao.henriques.32...@gmail.com wrote: Sarcasm perceptivity deficiency is a socially crippling disorder which renders the sufferer oblivious to sarcasm and leads him to treat sarcastic

Re: [gmx-users] Justifying 4fs production runs after 1fs equilibrations?

2014-02-11 Thread Mark Abraham
On Tue, Feb 11, 2014 at 12:11 PM, unitALX alec.zan...@gmail.com wrote: Helllo all! In my general situation, I have a batch of homology models that I would like to assess for stability by molecular dynamics. I am working with a postdoc in my lab who was extensive experience with NAMD, but

Re: [gmx-users] PBC problem after MD

2014-02-13 Thread Mark Abraham
If there's a problem, trjconv can handle it with the use of the right index groups, as suggested at http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions. But it can't keep these three things together if there's no index group that describes these three things. You may need

Re: [gmx-users] gromacs 4.6.4 query

2014-02-13 Thread Mark Abraham
On Thu, Feb 13, 2014 at 9:03 AM, Chaitali Chandratre chaitujo...@gmail.comwrote: Dear Sir, Thanks for your reply. With Change in host_config.h it worked fine. But It needed full Cuda folder to be copied into my home area. Can we compile gromacs-4.6.4 gpu version with *pgi* compiler?

Re: [gmx-users] Bonds/constraits betweeen two moleculetypes?

2014-02-17 Thread Mark Abraham
Hi, No. The traditional solution is to hack the two moleculetypes together, which involves some tedious renumbering. A good solution might be found if someone helps test the code in https://gerrit.gromacs.org/#/c/2566/. Mark On Mon, Feb 17, 2014 at 2:27 PM, Steven Neumann

Re: [gmx-users] Type of function for bond or bend in SPC/E or TIP3P model

2014-02-17 Thread Mark Abraham
Hi, Those water models are rigid, so the question doesn't really apply. But you can see in their .itp files what they would use if they were flexible, which tends to be the kind of thing you suggested. The bonded function type numbers can be looked up in tables in manual section 5.7, which

Re: [gmx-users] parameters problem

2014-02-17 Thread Mark Abraham
Seems like you're using cut-off electrostatics, which would be a good way of picking lottery numbers, and that's about all. Mark On Mon, Feb 17, 2014 at 10:16 AM, Nidhi Katyal nidhikatyal1...@gmail.comwrote: Dear all I am trying to simulate a protein in 3 steps: energy minimization (using

Re: [gmx-users] Type of function for bond or bend in SPC/E or TIP3P model

2014-02-18 Thread Mark Abraham
wrote: Thanks Mark. Could you send me the reference that SPC/E is a rigid model? I heard that SPC/E is a flexible model and I am doing simulation with gromacs and CP2K with this model without constraint. Regards, Leila On Mon, Feb 17, 2014 at 2:36 PM, Mark Abraham mark.j.abra...@gmail.com

Re: [gmx-users] g_cluster failing

2014-02-18 Thread Mark Abraham
Building all-against-all matrices takes a lot of memory, and if it runs out, then crazy things happen. I suggest you start with versions of your trajectories sampled very sparsely so there are few tens of samples, and get a sane result from g_cluster from that. Then scale up / find a lot of memory

Re: [gmx-users] g_principal -- bug or very bad choice of filenames

2014-02-18 Thread Mark Abraham
It shows as active to me... Mark On Tue, Feb 18, 2014 at 11:46 PM, Antonio Baptista bapti...@itqb.unl.ptwrote: On Fri, 7 Feb 2014, Justin Lemkul wrote: On 2/7/14, 6:08 PM, Antonio Baptista wrote: Dear all, This is a follow-up to an old thread on g_principal, which continues (as of

Re: [gmx-users] Fwd: Segmentation fault with mdrun

2014-02-20 Thread Mark Abraham
My only guess is that your compiler and/or MPICH version are broken. We certainly don't test on it. There's many reasons the install guide for 4.6 says to get the latest version of your compiler of choice. Mark On Thu, Feb 20, 2014 at 12:35 PM, Pavan Kumar kumar.pavan...@gmail.comwrote:

Re: [gmx-users] Is it possible to output the force/energy associated with each position restraint?

2014-02-20 Thread Mark Abraham
Only by constructing matching .tpr and trajectory subsets (tpbconv -n and trjconv -n) and then using mdrun -rerun to get the position restraint re-calculation to refer to only one. Mark On Thu, Feb 20, 2014 at 4:28 AM, Justin Lemkul jalem...@vt.edu wrote: On 2/19/14, 7:39 PM, Ling Liu

Re: [gmx-users] Guidance on how to install Gromacs-5.0-beta2

2014-02-22 Thread Mark Abraham
Yes. Or you could have tried it to see! :-) Mark On Feb 22, 2014 8:04 AM, Yogendra Ramtirtha ramtirtha.yogen...@gmail.com wrote: Actually, I used the build directory which was created earlier. Should I create a new build directory all over again ? Can you please guide me. Thanks On Sat,

Re: [gmx-users] conversion xtc to xyz format with openbabel

2014-02-22 Thread Mark Abraham
On Sat, Feb 22, 2014 at 10:16 PM, Dr. Vitaly Chaban vvcha...@gmail.comwrote: The workaround is to trjconv -o 111.pdb, open an editor, select a block of coordinates, and paste in XYZ file. I also do not like PDB files from gromacs, but AFAIK many programs generate such PDB files which other

Re: [gmx-users] Long trajectory split

2014-02-23 Thread Mark Abraham
Normally an MPI-enabled mdrun would be named mdrun_mpi, and running a non-MPI mdrun would produce symptoms like yours depending exactly how your filesystem chooses to do things, so Justin and Vitaly's theory is sound. Look at the top section of your .log file for what mdrun thinks about MPI! Mark

Re: [gmx-users] conversion xtc to xyz format with openbabel

2014-02-23 Thread Mark Abraham
formats such as xtc or dcd. Stéphane Abel, PhD CEA Saclay DSV/IbItec-S/SB2SM CNRS UMR 8221 Bat 528 Door 138C Gif-sur-Yvette, F-91191 FRANCE Phone (portable) : +33 6 49 37 70 60 -- Message: 5 Date: Sat, 22 Feb 2014 23:23:03 +0100 From: Mark Abraham

Re: [gmx-users] Temperature coupling

2014-02-23 Thread Mark Abraham
Hi, Unfortunately, there is a fair bit of code in GROMACS that only the author understands (if that many). Do have a look for any primary literature e.g. cited from the manual. But you may need to identify and read the relevant code fragment, unless you can devise a test of whether your

Re: [gmx-users] REMD slow's down drastically

2014-02-24 Thread Mark Abraham
Adding replicas cannot of itself slow things down, though it will increase the cost linearly. Don't try to run them all on the same amount of hardware as a smaller calculation! You are shooting yourself in the foot if you do not have at least one processor per replica (= MPI rank). Mark On Mon,

Re: [gmx-users] Single or Double precision

2014-02-24 Thread Mark Abraham
Yes, although the mismatch will typically be noted in the output. Mark On Mon, Feb 24, 2014 at 1:30 PM, Mostafa Javaheri m.javah...@gu.ac.irwrote: Dear Justin I minimized and equilibrated (em, nvt and npt) my protein by the single-precision GROMACS 4.5.3 version and then made final

Re: [gmx-users] gromacs5.0-beta2 version installing error

2014-02-24 Thread Mark Abraham
Hi, Thanks, we have fixed this issue. You can drop this file into its subdirectory to fix this for now. https://github.com/gromacs/gromacs/blob/master/src/contrib/fftw/CMakeLists.txt On Feb 24, 2014 5:37 PM, JuYeon ju8...@hotmail.com wrote: hi gromacs-users i downloaded

Re: [gmx-users] REMD slow's down drastically

2014-02-24 Thread Mark Abraham
On Feb 24, 2014 11:01 PM, Christopher Neale chris.ne...@alum.utoronto.ca wrote: Presuming that you have indeed set up the number of processors correctly (should be running on a different number of cored for different number of replicas to do a fair test), could it be a thread pinning issue?

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