Re: [gmx-users] Diffusion/PBC

Hi Debashis, Makes sure that the anion and receptor are together in the reference structure you use for trjconv -pbc nojump Cheers, Tsjerk On Tue, Nov 5, 2013 at 8:12 AM, Debashis Sahu wrote: > Dear All, > I have an problem related to jumping trajectory. In my MD > run, there is

[gmx-users] Re: Using mpirun on CentOS 6.0

Hi, I am getting the following error while using the command - [root@localhost INGT]# mpirun -np 24 mdrun_mpi -v -deffnm npt Error - /usr/bin/mpdroot: open failed for root's mpd conf filempiexec_localhost.localdomain (__init__ 1208): forked process failed; status=255 I complied gromacs using -

[gmx-users] free energy

Dear GMX Users I am using parmbsc0 force field to study DNA-ligand interaction but my problem is free energy calculation (MMPBSA) for this interaction. How can I calculate free energy using MMPBSA approach? Thank you very much for your time and consideration. Best Regards Kiana  -- gmx-user

[gmx-users] extra gro file generation

Dear all, I'm going to perform a molecular dynamics simulation on a protein. As a default the simulation gives one final *.gro file. I need to get a .gro file after each say 500 ps of my simulation, in addition of the final file. How can I do so? Best regards, Sarah Keshavarz -- gmx-users mailin

Re: [gmx-users] extra gro file generation

Dear Sarah, you have to use the trjconv command with the flags -b -e and -sep. For example: trjconv -f xxx.trr -s xxx.tpr -o out.gro -b (initial frame to read in ps) -e (last frame to read in ps) -sep Regards El mar, 05-11-2013 a las 01:04 -0800, sarah k escribió: > Dear all, > > I'm going to perf

Re: [gmx-users] choosing force field

Just out of curiosity -why can you only choose between GROMOS force fields? 2013/11/5 pratibha kapoor > Dear all > > I would like to carry out unfolding simulations of my dimeric protein and > would like to know which is the better force field to work with out of > gromos 96 43 or 53? Also, is

Re: [gmx-users] Gromacs-4.6 on two Titans GPUs

My suggestions: 1) During compilstion using -march=corei7-avx-i I have obtained error that somethng now found ( sorry I didnt save log) so I compile gromacs without this flag 2) I have twice as better performance using just 1 gpu by means of mdrun -ntmpi 1 -ntomp 12 -gpu_id 0 -v -deffnm md_CaM_

[gmx-users] Energy minimization has stopped....

Hi, Whenever I am trying to do position retrained MD run, It has been stopped at middle of the MD run. I have given the following error. Can you please suggest me something to resolve this error? Energy minimization has stopped, but the forces havenot converged to the requested precision Fmax < 1

Re: [gmx-users] Gromacs-4.6 on two Titans GPUs

Dear James, On 05/11/13 11:16, James Starlight wrote: My suggestions: 1) During compilstion using -march=corei7-avx-i I have obtained error that somethng now found ( sorry I didnt save log) so I compile gromacs without this flag 2) I have twice as better performance using just 1 gpu by means o

Re: [gmx-users] extra gro file generation

On 05.11.2013 10:04, sarah k wrote: I'm going to perform a molecular dynamics simulation on a protein. As a default the simulation gives one final *.gro file. I need to get a .gro file after each say 500 ps of my simulation, in addition of the final file. How can I do so? Riccardo already gave t

Re: [gmx-users] Gromacs-4.6 on two Titans GPUs

Dear Richard, 1) mdrun -ntmpi 1 -ntomp 12 -gpu_id 0 -v -deffnm md_CaM_test gave me performance about 25ns/day for the explicit solved system consisted of 68k atoms (charmm ff. 1.0 cutoofs) gaves slightly worse performation in comparison to the 1) finally 3) mdrun -deffnm md_CaM_test running

Re: [gmx-users] Energy minimization has stopped....

What does your curve look like? What parameters are you using in the mdp? How big is your system and what kind of molecules are in there? Providing this kind of information would help people work out what the problem is. Then again it may be ok that the minimisation has converged without reaching

Re: [gmx-users] Energy minimization has stopped....

On 11/5/13 6:28 AM, Kalyanashis Jana wrote: Hi, Whenever I am trying to do position retrained MD run, It has been stopped at middle of the MD run. I have given the following error. Can you please suggest me something to resolve this error? Energy minimization has stopped, but the forces have

Re: [gmx-users] free energy

On 11/5/13 3:45 AM, kiana moghaddam wrote: Dear GMX Users I am using parmbsc0 force field to study DNA-ligand interaction but my problem is free energy calculation (MMPBSA) for this interaction. How can I calculate free energy using MMPBSA approach? Thank you very much for your time and c

[gmx-users] Re: Energy minimization has stopped....

I have given my .mdp file, ; title = trp_drg warning = 10 cpp = /usr/bin/cpp define = -DPOSRES constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps = 100 ; total 2000.0 ps. ns

Re: [gmx-users] Energy minimization has stopped....

Dear Justin, Can you please tell me, how I can solve this problem?? If I will change the coordinate of atom 15461, will it help me? But you know, I did this step changing the position of drug molecule and I got same error. On Tue, Nov 5, 2013 at 5:44 PM, Justin Lemkul wrote: > > > On 11/5/13

Re: [gmx-users] Re: Energy minimization has stopped....

On 11/5/13 7:19 AM, Kalyanashis wrote: I have given my .mdp file, ; title = trp_drg warning = 10 cpp = /usr/bin/cpp define = -DPOSRES constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps

Re: [gmx-users] Energy minimization has stopped....

On 11/5/13 7:31 AM, Kalyanashis Jana wrote: Dear Justin, Can you please tell me, how I can solve this problem?? If I will change the coordinate of atom 15461, will it help me? But you know, I did this step changing the position of drug molecule and I got same error. You should first do wh

[gmx-users] mdrun

Dear Users, I am running MD simulations of a protein-ligand system. Sometimes when i do an mdrun, be it for the energy minimization or during the nvt and npt equillibration or the actual md run step, sometimes the output files are named in a very odd way (strange extensions) e.g em.gro.tprr or md.

Re: [gmx-users] mdrun

On 11/5/13 7:37 AM, MUSYOKA THOMMAS wrote: Dear Users, I am running MD simulations of a protein-ligand system. Sometimes when i do an mdrun, be it for the energy minimization or during the nvt and npt equillibration or the actual md run step, sometimes the output files are named in a very odd

Re: [gmx-users] free energy

Dear Kiana, You can contact with Paissoni Cristina (email: paissoni.crist...@hsr.it) to get tool using MM/PBSA with GROMACS. Hope it help :) Cheers, Kieu Thu On Tue, Nov 5, 2013 at 7:18 PM, Justin Lemkul wrote: > > > On 11/5/13 3:45 AM, kiana moghaddam wrote: > >> Dear GMX Users >> >> >> >> I

Re: [gmx-users] mdrun

Dear Dr Justin, Much appreciation. You nailed it. Kind regards. On Tue, Nov 5, 2013 at 2:41 PM, Justin Lemkul wrote: > > > On 11/5/13 7:37 AM, MUSYOKA THOMMAS wrote: > >> Dear Users, >> I am running MD simulations of a protein-ligand system. Sometimes when i >> do >> an mdrun, be it for the ene

[gmx-users] CHARMM .mdp settings for GPU

Dear All, I intend to run a membrane-protein system in GPU. I am slightly confused about the .mdp settings Non-gpu settings (according to original CHARMM FF paper): rlist = 1.0 rlistlong= 1.4 rvdw_switch = 0.8 vdwtype= Switch coulombty

Re: [gmx-users] Gromacs-4.6 on two Titans GPUs

On Tue, Nov 5, 2013 at 12:55 PM, James Starlight wrote: > Dear Richard, > > > 1) mdrun -ntmpi 1 -ntomp 12 -gpu_id 0 -v -deffnm md_CaM_test > gave me performance about 25ns/day for the explicit solved system consisted > of 68k atoms (charmm ff. 1.0 cutoofs) > > gaves slightly worse performation i

[gmx-users] Re: Replacing atom

Hi, I need to replace an atom with another in the considered system. I'd like to know if it is possible and if so what changes I need to do. thanks j.rahrow On Thu, Oct 31, 2013 at 12:47 PM, J Alizadeh wrote: > Hi, > I need to replace an atom with another in the considered system. > I'd li

Re: [gmx-users] Re: Hardware for best gromacs performance?

29420 Atoms with a some tuning of the write out and communication intervals: nodes again: 2 x Xeon E5-2680v2 + 2 x NVIDIA K20X GPGPUs @ 4fs vsites 1 node 212 ns/day 2 nodes 295 ns/day -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please

Re: [gmx-users] extra gro file generation

Dear Riccardo Concu and Mirco Wahab, Thanks for your perfect responses. Regards, Sarah -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Plea

Re: [gmx-users] Re: Replacing atom

On 11/5/13 10:34 AM, J Alizadeh wrote: Hi, I need to replace an atom with another in the considered system. I'd like to know if it is possible and if so what changes I need to do. The coordinate file replacement is trivial. Just open the file in a text editor and repname the atom. The top

Re: [gmx-users] Gentle heating with implicit solvent

I wonder whether increasing the surface tension parameter sa-surface-tension might solve the problem with the protein unfolding. Thanks, Gianluca On Mon, 4 Nov 2013, Gianluca Interlandi wrote: Hi Justin, We are using infinite cutoffs (all vs all). Here is the mdp file for the heating

Re: [gmx-users] Re: Using gromacs on Rocks cluster

You need to configure your MPI environment to do so (so read its docs). GROMACS can only do whatever that makes available. Mark On Tue, Nov 5, 2013 at 2:16 AM, bharat gupta wrote: > Hi, > > I have installed Gromcas 4.5.6 on Rocks cluster 6.0 andmy systme is having > 32 processors (cpu). But whi

Re: [gmx-users] Re: Hardware for best gromacs performance?

Timo, Have you used the default settings, that is one rank/GPU? If that is the case, you may want to try using multiple ranks per GPU, this can often help when you have >4-6 cores/GPU. Separate PME ranks are not switched on by default with GPUs, have you tried using any? Cheers, -- Szilárd Páll

[gmx-users] Re: Gromacs-4.6 on two Titans GPUs

Hi Mike, I have similar configurations except a cluster of AMD-based linux platforms with 2 GPU cards. Your suggestion works. However, the performance of 2 GPU discourages me because , for example, with 1 GPU, our computer node can easily obtain a simulation of 31ns/day for a protein of

[gmx-users] Re: Hardware for best gromacs performance?

Hi Timo, Can you provide a benchmark with "1" Xeon E5-2680 with "1" Nvidia k20x GPGPU on the same test of 29420 atoms ? Are these two GPU cards (within the same node) connected by a SLI (Scalable Link Interface) ? Thanks, Dwey -- View this message in context: http://gromacs.5086.x6.nab

Re: [gmx-users] Re: Gromacs-4.6 on two Titans GPUs

Hi Dwey, First and foremost, make sure to read the http://www.gromacs.org/Documentation/Acceleration_and_parallelization page, in particular the "Multiple MPI ranks per GPU" section which applies in your case. Secondly, please do post log files (pastebin is your friend), the performance table at

Re: [gmx-users] Re: Hardware for best gromacs performance?

On Tue, Nov 5, 2013 at 9:55 PM, Dwey Kauffman wrote: > Hi Timo, > > Can you provide a benchmark with "1" Xeon E5-2680 with "1" Nvidia > k20x GPGPU on the same test of 29420 atoms ? > > Are these two GPU cards (within the same node) connected by a SLI (Scalable > Link Interface) ? Note that

[gmx-users] Re: Gromacs-4.6 on two Titans GPUs

Hi Szilard, Thanks for your suggestions. I am indeed aware of this page. In a 8-core AMD with 1GPU, I am very happy about its performance. See below. My intention is to obtain a even better one because we have multiple nodes. ### 8 core AMD with 1 GPU, Force evaluation time GPU/CPU: 4.006 ms

[gmx-users] Re: Hardware for best gromacs performance?

Hi Szilard, Thanks. >From Timo's benchmark, 1 node142 ns/day 2 nodes FDR14 218 ns/day 4 nodes FDR14 257 ns/day 8 nodes FDR14 326 ns/day It looks like a infiniband network is "required" in order to scale up when running a task across nodes. Is it correct ? Dwey -- View t

RE: [gmx-users] RE: Gibbs Energy Calculation and charges

Thank you for the pointer Michael. couple-intramol = no What a diff of the output from gmxdump of the two tpr files shows is in both of these cases (normal and double charged), when: lambda is set to 1.0 (atoms within both molecules will have zero charge) lambda is set to 0.00 and

[gmx-users] RE: Gibbs Energy Calculation and charges

Thanks for the suggestion Chris. Had a quick look and can't see easily how to do this, but I think I am at a point now where it is not an issue and don't have to actually do this. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, M

[gmx-users] Re: gmx-users Digest, Vol 115, Issue 16

Message: 5 Date: Mon, 04 Nov 2013 13:32:52 -0500 From: Justin Lemkul Subject: Re: [gmx-users] Analysis tools and triclinic boxes To: Discussion list for GROMACS users Message-ID: <5277e854.9000...@vt.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hi Justin, Thanks for the resp

[gmx-users] Re: Hardware for best gromacs performance?

Hi Szilárd and all, Thanks very much for the information. I am more interested in getting single simulations to go as fast as possible (within reason!) rather than overall throughput. Would you expect that the more expensive dual Xeon/Titan systems would perform better in this respect? Cheers

Re: [gmx-users] Re: Hardware for best gromacs performance?

Yes, that has been true for GROMACS for a few years. Low-latency communication is essential if you want a whole MD step to happen in around 1ms wall time. Mark On Nov 5, 2013 11:24 PM, "Dwey Kauffman" wrote: > Hi Szilard, > > Thanks. > > >From Timo's benchmark, > 1 node142 ns/day > 2

Re: [gmx-users] Diffusion/PBC

Your best bet is probably to center everything on the receptor. That will prevent jumping of the receptor only, which is hopefully all you need. -Trayder On Tue, Nov 5, 2013 at 7:14 PM, Tsjerk Wassenaar wrote: > Hi Debashis, > > Makes sure that the anion and receptor are together in the refere

Re: [gmx-users] g_lie and ligand only simulation

Dear users, When the simulation was carried out with PME rcoulomb was set equal to rlist. But when I need to to ligand-water simulation without PME (with RF-0) then it requires rlist greater by 0.1-0.3 than rcoulomb. So if I rerun protein-ligand-water simulation there could be more differences in