[gmx-users] Question about switching off non-bonded interactions between two molecules for MD simulation

Dear GROMACS users, I am new to GROMACS software and have a question about switching off pair-wise non-bonded interactions between two molecules. I have a simulation box composed of a protein with a substrate inside the protein catalytic pocket and there are no covalent bonds between protein

Re: [gmx-users] slurm, gres:gpu, only 1 GPU out of 4 is detected

I had the misconception that I have to set gpuid by CUDA_VISIBLE_DEVICES set by slurm. However, slurm exposes the gpu for gromacs by a different mechanism. On 11/13/19 4:55 PM, Tamas Hegedus wrote: Hi, I run gmx 2019 using GPU There are 4 GPUs in my GPU hosts. I have slurm and configured

[gmx-users] slurm, gres:gpu, only 1 GPU out of 4 is detected

Hi, I run gmx 2019 using GPU There are 4 GPUs in my GPU hosts. I have slurm and configured gres=gpu 1. If I submit a job with --gres=gpu:1 then GPU#0 is identified and used (-gpu_id $CUDA_VISIBLE_DEVICES). 2. If I submit a second job, it fails: the $CUDA_VISIBLE_DEVICES is 1 and selected, but

Re: [gmx-users] eelctric field

Dear Christian, Thank you for your reply. However, still it is not fully clear to me. Lets only talk about gmx energy. How it happens that I get from gmx energy similar values of energies (LJ, columbs, total energies) while a different pressure, with and without applied filed? The total energy

Re: [gmx-users] eelctric field

Hello Amin, When you apply an electric field during the simulation by setting the mdp parameters like E-x =... as you describe, nothing more happens than that each atom experiences an additional force that is "atom charge * field strength". The energy terms or virial (that then would relate

Re: [gmx-users] eelctric field

sorry I use gromacs/2016.1. On Wed, Nov 13, 2019 at 2:44 PM Amin Rouy wrote: > Hi, > > I am using gromacs 5.0.4. I apply a uniform electric field in x direction > of my box (no walls), > E-x= 1 10 0, and simulation runs without error. > I notice that the values of electrostatic interactions I

[gmx-users] eelctric field

Hi, I am using gromacs 5.0.4. I apply a uniform electric field in x direction of my box (no walls), E-x= 1 10 0, and simulation runs without error. I notice that the values of electrostatic interactions I get from the simulation is the same as without the an electric field. Which is strange,

[gmx-users] gmx rdf with surf option

Dear GMX users, I have a question regarding GMX RDF and I apologize if my question is too basic. My trajectory consists of a dimer inserted in a membrane with an explicit water/ion environment. I would like to compute the distribution of the center of mass of lipid molecules to the surface of

Re: [gmx-users] (no subject)

thanks Prof. Justin On Tue, Nov 12, 2019 at 8:48 PM Justin Lemkul wrote: > > Please use an appropriate subject line. > > On 11/12/19 5:29 AM, shakuntala dhurua wrote: > > hello, > > Here I want to generate arg.pdb to arg.gro by using amber99sb force > field . > > for test i have used 1 residue

Re: [gmx-users] (no subject)

thanks Bratin for your suggestion On Tue, 12 Nov 2019, 7:54 pm Bratin Kumar Das, <177cy500.bra...@nitk.edu.in> wrote: > I think you have capped your residue in the N-terminal and C-terminal > end...and the capping is not defined in your .rtp entry.. that's why this > error is coming > > On Tue

Re: [gmx-users] How to produce "gro" format for calcite {1014} structure.

Hi, Maybe you could try to convert the cif format to pdb format, if you feel that your conversion from cif to gro format is not working. Best regards Alessandra On Tue, Nov 12, 2019 at 5:09 PM Hamid Zaree wrote: > Hi. > I would like to simulate Calcite structure in GROMACS. How could I make the