Re: [gmx-users] Domain decomposition error while running coarse grained simulations on cluster

On 9/3/19 12:21 PM, Avijeet Kulshrestha wrote: Hi Justin, Thanks for replying to my query. Please see the error message below of log file. I have user-defined bonded, angle potential which I am providing by supplying tabulated data. I have position restraint also on backbone atoms of the

Re: [gmx-users] The problem of utilizing multiple GPU

Hello Mark Abraham, Thank you very much for your reply. I will definitely check the webinar and gromacs document. But now I am confused and expect an direct solution. The workstation should have 18 cores each with 4 hyperthreads. The output of "lscpu" reads: Architecture: x86_64 CPU

[gmx-users] Question about the pulling code

Dear All, I want to pulling a ligand out of the binding pocket using Gromacs 2019. The pulling code was: pull= yes pull_ncoords= 1 pull_coord1_type= umbrella pull_coord1_geometry= direction pull_ngroups= 1 pull_group1_name=

[gmx-users] how to define a pair

Hi, I am performed a all-atom simulation of a membrane-protein system (the starting structure received from CHARMM-GUI server, using charmm36 FF).  #include "toppar/charmm36.itp"   [ defaults ]; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ1 2 yes 1.0 1.0 I want to add a pair between list of two

[gmx-users] how to define a pair

Hi, I am performed a all-atom simulation of a membrane-protein system (the starting structure received from CHARMM-GUI server, using charmm36 FF).  #include "toppar/charmm36.itp" [ defaults ] ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 1 2 yes 1.0 1.0 I want to add a pair between list of two

Re: [gmx-users] The problem of utilizing multiple GPU

Hi, On Wed, 4 Sep 2019 at 12:54, sunyeping wrote: > Dear everyone, > > I am trying to do simulation with a workstation with 72 core and 8 geforce > 1080 GPUs. > 72 cores, or just 36 cores each with two hyperthreads? (it matters because you might not want to share cores between simulations,

[gmx-users] The problem of utilizing multiple GPU

Dear everyone, I am trying to do simulation with a workstation with 72 core and 8 geforce 1080 GPUs. When I do not assign a certain GPU with the command: gmx mdrun -v -deffnm md all GPUs are used and but the utilization of each GPU is extremely low (only 1-2 %), and the simulation will be

Re: [gmx-users] REMD-error

Thank you for your email sir. On Wed, Sep 4, 2019 at 2:42 PM Mark Abraham wrote: > Hi, > > On Wed, 4 Sep 2019 at 10:47, Bratin Kumar Das <177cy500.bra...@nitk.edu.in > > > wrote: > > > Respected Mark Abraham, > > The command-line and the job > >

[gmx-users] Channelrhodopsin topology

Hello everyone, I got some troubles with topology setup for channelrhodopsin setup in membrane. It is first such difficult system I met at my short scientific way and in fact it blocks my progress. I am not sure if gromacs mailing list is the way I should call for help, but perhaps I

Re: [gmx-users] REMD-error

Hi, On Wed, 4 Sep 2019 at 10:47, Bratin Kumar Das <177cy500.bra...@nitk.edu.in> wrote: > Respected Mark Abraham, > The command-line and the job > submission script is given below > > #!/bin/bash > #SBATCH -n 130 # Number of cores > Per the docs, this is

Re: [gmx-users] REMD-error

Respected Mark Abraham, The command-line and the job submission script is given below #!/bin/bash #SBATCH -n 130 # Number of cores #SBATCH -N 5 # no of nodes #SBATCH -t 0-20:00:00 # Runtime in D-HH:MM #SBATCH -p cpu # Partition to submit to #SBATCH -o

Re: [gmx-users] REMD-error

Hi, We need to see your command line in order to have a chance of helping. Mark On Wed, 4 Sep 2019 at 05:46, Bratin Kumar Das <177cy500.bra...@nitk.edu.in> wrote: > Dear all, > I am running one REMD simulation with 65 replicas. I am using > 130 cores for the simulation. I am