Re: [gmx-users] cpu/gpu utilization

>(try the other parallel modes) Do you mean OpenMP and MPI? >- as noted above try offloading only the nonbondeds (or possibly the hybrid >PME mode -pmefft cpu) May I know how? Which part of the documentation says about that? Regards, Mahmood -- Gromacs Users mailing list * Please search t

[gmx-users] An atom is beyond the wall in gromacs2018

Hi Gromacs Users I did a simulated annealing MD with gromacs/5.0.1 and gromacs/2018. In both cases I had the same input configuration and parameters for the potential wall. The simulation with gromacs/5.0.1 did achieve convergence but with the gromacs/2018, an atom always go beyond the wall. Can s

Re: [gmx-users] cpu/gpu utilization

PS: Care to know what can you do? - as noted above try offloading only the nonbondeds (or possibly the hybrid PME mode -pmefft cpu) - check if your GPU has application clocks that can be bumped - if you have the means, consider getting a bit faster GPU; the Quadro M2000 in your machine is both slig

Re: [gmx-users] cpu/gpu utilization

Thanks! Looking at the log file, as I guessed earlier, you can see the following: - Given that you have a rather low-end GPU and a fairly fast workstation CPU the run is *very* GPU-bound: the CPU spends 16.4 + 54.2 = 70.6% waiting for the GPU (see lines 628 and 630) - this means that the default

Re: [gmx-users] cpu/gpu utilization

>The list does not accept attachments, so please use a file sharing or content >sharing website so >everyone can see your data and has the context. I uploaded here https://pastebin.com/RCkkFXPx Regards, Mahmood -- Gromacs Users mailing list * Please search the archive at http://www.gromac

Re: [gmx-users] cpu/gpu utilization

The list does not accept attachments, so please use a file sharing or content sharing website so everyone can see your data and has the context. -- Szilárd On Wed, Feb 28, 2018 at 7:51 PM, Mahmood Naderan wrote: > >Additionally, you still have not provided the *mdrun log file* I > requested. to

[gmx-users] Pressure using solvation shell

Dear Gromacs Users, I am using a solvation shell (-shell command) around a large nucleosome system to accelerate the simulation speed, and was wondering what ensemble is suggested to run such a system in a solvation shell? After a few trial runs using NPT equilibration with and without constr

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 166, Issue 129

Hi Justin, I did try to reproduce the behavior of the GPU-calculation crash with a vanilla gromacs (5.1.4) version. No matter if I use vanilla gromacs or the patched gromacs version I do see that on CPU node only the calculation runs without problems, as soon as I try to run the simulation with GP

Re: [gmx-users] cpu/gpu utilization

>Additionally, you still have not provided the *mdrun log file* I requested. >top output is not what I asked for. See the attached file. Regards, Mahmood -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting

Re: [gmx-users] Backup files

Hi, Setting GMX_MAXBACKUP=-1 is as easy as it can get :-) Mark On Wed, Feb 28, 2018 at 7:03 PM Mahmood Naderan wrote: > Well I searched for "gromacs backoff" first and then while googling I saw > [1] and an environment variable GMX_MAXBACKUP [2]. > > > [1] http://cupnet.net/clean-gromacs-backu

Re: [gmx-users] cpu/gpu utilization

Your run is probably GPU-bound because you have a rather slow GPU and as per new mdrun defaults both PME and nonbondeds are offloaded which may not be ideal for your case. Try the different offload modes to see which one is best on your hardware. Additionally, you still have not provided the *mdru

Re: [gmx-users] Gromacs on CPU runs fine, same calculation crashes on GPU with nonbonded interaction larger than table limit

On 2/28/18 1:13 PM, Marc Hoemberger wrote: Hi everyone, I ran a targeted md simulation with gromacs 5.1.4 + plumed 2.4.0 on a 32-core node. The simulation worked well, however when I wanted to try to run the identical simulation (same starting points etc) on a CPU/GPU node the run crashes with

Re: [gmx-users] Backup files

Well I searched for "gromacs backoff" first and then while googling I saw [1] and an environment variable GMX_MAXBACKUP [2]. [1] http://cupnet.net/clean-gromacs-backups [2] Environment Variables — GROMACS 5.1 documentation Therefore I asked for a simpler method ;) Anyway... Regards, Mahmood

[gmx-users] Gromacs on CPU runs fine, same calculation crashes on GPU with nonbonded interaction larger than table limit

Hi everyone, I ran a targeted md simulation with gromacs 5.1.4 + plumed 2.4.0 on a 32-core node. The simulation worked well, however when I wanted to try to run the identical simulation (same starting points etc) on a CPU/GPU node the run crashes with two warnings of the following type: WARNING:

Re: [gmx-users] Backup files

There's an even better solution in the GROMACS documentation, which e.g. googling "disable gromacs backups" will find ;-) Mark On Wed, Feb 28, 2018 at 4:50 PM András Ferenc WACHA wrote: > Dear Mahmood, > > as far as I know, each command supports the "-nobackup" command line > switch... > > Best

Re: [gmx-users] cpu/gpu utilization

I forgot to say that gromacs reports No option -multi Using 1 MPI thread Using 16 OpenMP threads 1 GPU auto-selected for this run. Mapping of GPU IDs to the 2 GPU tasks in the 1 rank on this node:   PP:0,PME:0 NOTE: GROMACS was configured without NVML support hence it can not exploit   appli

Re: [gmx-users] Backup files

Yes you are right. Thank you very much. Regards, Mahmood On Wednesday, February 28, 2018, 7:19:55 PM GMT+3:30, András Ferenc WACHA wrote: Dear Mahmood, as far as I know, each command supports the "-nobackup" command line switch... Best regards, Andras -- Gromacs Users mailin

Re: [gmx-users] Backup files

Dear Mahmood, as far as I know, each command supports the "-nobackup" command line switch... Best regards, Andras On 02/28/2018 04:46 PM, Mahmood Naderan wrote: > Hi,How can I disable the backup feature? I mean backed up files which start > and end with # character. > > Regards, > Mahmood --

[gmx-users] Backup files

Hi,How can I disable the backup feature? I mean backed up files which start and end with # character. Regards, Mahmood -- 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

Re: [gmx-users] cpu/gpu utilization

By runing gmx mdrun -nb gpu -deffnm md_0_1 I see the following outputs $ top -b  | head -n 10 top - 19:14:10 up 7 min,  1 user,  load average: 4.54, 1.40, 0.54 Tasks: 344 total,   1 running, 343 sleeping,   0 stopped,   0 zombie %Cpu(s):  7.1 us,  0.5 sy,  0.0 ni, 91.9 id,  0.4 wa,  0.0 hi,  0.0

Re: [gmx-users] generating Topology file of Metal Oxide

It is doable, we have just finished a study (not published yet) of TiO2 nanoparticles oriented attachment. But like Justin told you, GROMACS does not have any native support for that kind of system, so you're on your own to build topologies and to extract information from the trajectories (GROMACS

Re: [gmx-users] generating Topology file of Metal Oxide

On 2/28/18 7:14 AM, Kanwal Gill wrote: Respected sir/ madam, I start MD silmulations with metal oxides but failed to generate its topology file. i also checked with diferent softwares like PRODRG or ATB, but do not get the topology file. please suggest me the solution. GROMACS probably isn't

Re: [gmx-users] How to use LENNARD JONES 9-6 potential form in GROMACS

On 2/28/18 12:15 AM, sanjeet kumar singh ch16d012 wrote: Hello List, Can anyone tell me regarding how can i use Lennard Jones 9-6 potential form in GROMACS. You can use a tabulated potential. -Justin -- == Justin A. Lemkul, Ph.D. As

Re: [gmx-users] Equilibration

On 2/28/18 6:38 AM, Amin Rouy wrote: Thanks Justin, however, I run a simulation of a solute in water. I have 2 question please: 1- After NVT equilibrium, I see that all quantities like energies and temperature become stable, except pressure. Should I continue

[gmx-users] generating Topology file of Metal Oxide

Respected sir/ madam, I start MD silmulations with metal oxides but failed to generate its topology file. i also checked with diferent softwares like PRODRG or ATB, but do not get the topology file. please suggest me the solution. Kanwal. -- Gromacs Users mailing list * Please search the archiv

Re: [gmx-users] Equilibration

Thanks Justin, however, > >> I run a simulation of a solute in water. I have 2 question please: >> >> 1- After NVT equilibrium, I see that all quantities like energies and >> temperature become stable, except pressure. Should I continue till >> pressure >> also goes stable? or can I move forward a

Re: [gmx-users] Equilibration

sorry but I did not get my answer. In NVT equilibration, the pressure is not equilibrated yet, can I move forward to production run? (I see that I have no blow up when I run production) On Wed, Feb 28, 2018 at 10:38 AM, Quyen V. Vu wrote: > No matter how many steps of equilibration you want to r

Re: [gmx-users] Equilibration

No matter how many steps of equilibration you want to run. You need to run production run when your configuration is reasonable and in which condition, which ensemble you want to mimic On Wed, Feb 28, 2018 at 3:54 PM, Amin Rouy wrote: > Hi, > > > I run a simulation of a solute in water. I have 2

[gmx-users] Equilibration

Hi, I run a simulation of a solute in water. I have 2 questions please: 1- After NVT equilibrium, I see that all quantities like energies and temperature become stable, except pressure. Should I continue untill pressure becomes stable too? or can I move forward and do it in production run? 2-

[gmx-users] An atom is beyond the wall in gromacs2018

Hi Gromacs Users I did a simulated annealing MD with gromacs/5.0.1 and gromacs/2018. In both cases I had the same input configuration and parameters for the potential wall. The simulation with gromacs/5.0.1 did achieve convergence but with the gromacs/2018, an atom always go beyond the wall. Can so