Re: [gmx-users] regarding hydrogen bond correlation function for Cdd for TIP4P/2005 water model

Dear Erik, I tried unfolding the trajectory using trjconv -pbc nojump option as well. But I did not get the correct t^-3/2 scaling. I am using Gromacs version 4.6.5. Best regards, Abhinav On Wed, Sep 13, 2017 at 3:30 PM, Erik Marklund wrote: > Dear Abhinav, > > This

Re: [gmx-users] .XTC file could not be found after simulation completion

Yes, sorry mistake. nstxout-compressed = XXX ; write .xtc trajectory every XXX ps -- 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 *

Re: [gmx-users] Ionic liquid simulation problem

On 9/13/17 5:55 PM, Agatha Faria wrote: Dear GROMACS Community, I am very new with GROMACS I am trying to run a simulation of an ionic liquid (1-butyl-3-methyl-imidazolium and hexafluorophosphate) according to the following protocol: 1. Prepared the respective PDB files and added/modified

Re: [gmx-users] gmx insert-molecules not inserting molecules

On 9/13/17 5:54 AM, Souparno Adhikary wrote: We tried to simulate a small molecule using GROMACS. We generated the topology file and the GROMACS coordinate file using the PRODRG server. We optimized the molecule prior to generating topology using GAUSSIAN 09. Don't use PRODRG unless you

Re: [gmx-users] .XTC file could not be found after simulation completion

On 9/13/17 5:02 AM, Nikhil Maroli wrote: Hi, You need to add compressed-x-grps in mdp. You can convert trr to xtc if you need. compressed-x-grps has no effect without nstxout-compressed, which is the actual keyword to signal that mdrun should write an .xtc file. -Justin --

Re: [gmx-users] Fwd: Can a mutation make a protein stable - result analysis from GROMACs run

On 9/11/17 5:33 PM, Deep kumar wrote: Hello All, I ran a 10ns simulation on a wild and mutant type of a protein complex. Attached is the rmsf graph. "Green" is the mutant protein with mutation at residue 71 (marked) and "purple" is the wild protein. After looking at the graph can it be said

Re: [gmx-users] Crystallization of NaCl saturated aqueous solution under high temperature of low pressure.

On 9/11/17 1:05 PM, Yanke Peng wrote: Hi, Justin thanks again for your reply! 1. The 352 water molecules in a .gro file was actually gotten. I have checked it by viewing the .gro file and by the VMD and Avogrado software. 2. Could the failure be caused by the out-of-box hydrogen atoms? (Some

[gmx-users] Ionic liquid simulation problem

Dear GROMACS Community, I am very new with GROMACS I am trying to run a simulation of an ionic liquid (1-butyl-3-methyl-imidazolium and hexafluorophosphate) according to the following protocol: 1. Prepared the respective PDB files and added/modified the OPLS/AA force field parameters

Re: [gmx-users] performance

Hi Szilárd, Thanks again. I tried now with -multidir like this: mpirun -np 16 gmx_mpi mdrun -s test -ntomp 2 -maxh 0.1 -multidir t1 t2 t3 t4 So this runs 4 jobs on same node so for each job np is = 16/4, and each job using 2 GPU. I get now quite improved performance and equal performance for

Re: [gmx-users] performance

Hi, First off, have you considered options 2) using multi-sim? That would allow you to not have to bother manually set offsets. Can you not submit your jobs such that you fill at least a node? How many threads/cores does you node have? Can you share log files? Cheers, -- Szilárd On Wed, Sep

Re: [gmx-users] performance

Hi Szilárd, Sorry I was bit quick to say its working with pinoffset. I just submitted four same jobs (2 gpus, 4 nprocs) on the same node with -pin on and different -pinoffset to 0, 5, 10, 15 (numbers should be fine as there are 40 cores on node). Still I don't get same performance (all variably

Re: [gmx-users] performance

Hi Szilárd, Thanks, option 3 was in my mind but I need to figure out now how :) Manually fixing pinoffset as of now seems working with some quick test. I think option 1 would require to ask the admin but I can try option 3 myself. As there are other users from different places who may not bother

Re: [gmx-users] performance

J, You have a few options: * Use SLURM to assign not only the set of GPUs, but also the correct set of CPU cores to each mdrun process. If you do so, mdrun will respect the affinity mask it will inherit and your two mdrun jobs should be running on the right set of cores. This has the drawback

Re: [gmx-users] performance

Hi Szilárd, Thanks for your reply. This is useful but now am thinking because the slurm launches job in an automated way it is not really in my control to choose the node. So following things can happen; say for two mdrun jobs I set -pinoffset 0 and -pinoffset 4; - if they are running on the

Re: [gmx-users] performance

My guess is that the two jobs are using the same cores -- either all cores/threads or only half of them, but the same set. You should use -pinoffset; see: - Docs and example: http://manual.gromacs.org/documentation/2016/user-guide/mdrun-performance.html - More explanation on the thread pinning

Re: [gmx-users] performance

Sorry forgot to add; we thought the two jobs are using same GPU ids but cuda visible devices show both jobs are using different ids (0,1 and 2,3) - J On Wed, Sep 13, 2017 at 5:33 PM, gromacs query wrote: > Hi All, > > I have some issues with gromacs performance. There

[gmx-users] performance

Hi All, I have some issues with gromacs performance. There are many nodes and each node has number of gpus and the batch process is controlled by slurm. Although I get good performance with some settings of number of gpus and nprocs but when I submit same job twice on the same node then the

Re: [gmx-users] regarding hydrogen bond correlation function for Cdd for TIP4P/2005 water model

Dear Abhinav, This is a bit tricky. We implemented the geminate recombination model some time ago, but have taken it our of the gmx hbond tool because it complicates the code quite a lot. That said, if you want to use that old code you first need to "pbc-unwrap” your trajectory using trjconv

[gmx-users] gmx insert-molecules not inserting molecules

We tried to simulate a small molecule using GROMACS. We generated the topology file and the GROMACS coordinate file using the PRODRG server. We optimized the molecule prior to generating topology using GAUSSIAN 09. However, we tried to study the interaction between multiple copies of the same

[gmx-users] Differentiate of aggregation of precipitation in MD simulation

Dear all, I am simulation the aggregation of HULIS like molecule. However I would like know if there is way in Gromacs to analyse if these bunch of molecules gather together because of aggregation or precipitation? Bests -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] .XTC file could not be found after simulation completion

Hi, You need to add compressed-x-grps in mdp. You can convert trr to xtc if you need. -- 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

[gmx-users] .XTC file could not be found after simulation completion

HI, I could not find any .XTC file after completion of my simulation. My .mdp file for production run given below: integrator = md dt = 0.002 nsteps = 500 nstlog = 1000 nstxout = 5000 nstvout