[gmx-users] Fwd: atoms are not part of any of the T-Coupling groups

-- Forwarded message - From: ISHRAT JAHAN Date: Tue, May 7, 2019 at 11:05 AM Subject: atoms are not part of any of the T-Coupling groups To: Dear all, I am trying to calculate the lennard Jones interaction energy between protein and urea in the first solvation shell. I have

Re: [gmx-users] Error when compiling 2019.2 with -DGMX_MPI=ON

Realise I should provide some output etc for each of these: ## ## ## ## cmake .. -DGMX_MPI=OFF -DGMX_GPU=ON -DGMX_BUILD_MDRUN_ONLY=ON

[gmx-users] GROMOS 54A8 Force field

Dear users, Could you please suggest me where I can get the complete package of GROMOS 54A8 force filed developed by Prof. Dr. Chris Oostenbrink and co-worker ( https://pubs.acs.org/doi/10.1021/ct300156h). Looking forward to your suggestions. Thanks in advance. Sincerely yours, Kalyanashis Jana

Re: [gmx-users] how to change ps x axis format to ns in gyrate.xvg

Pest the full error message.. On Sun 5 May, 2019, 7:59 PM Ladan Mafakhe, wrote: > Hello > > I used below command gyrate to made gyrate.xvg file > > gmx gyrate -s md_0_1.tpr -f md_0_1_noPBC.xtc -o gyrate.xvg > The gyrate.xvg file was generated ps time scale but I want to generate > this

Re: [gmx-users] Membrane-protein Simulation

@email on Membrane protein Simulation: https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2019-May/125180.html Dear Najamuddin Memon Thanks for your reply. I am a little confused here. Why is the protein alone drifting? Typically, when we simulate protein only or protein-ligand

[gmx-users] Aggregate size

Hi, I am studying self assembly of peptide monomers via MD simulation. Can anyone suggest me regarding the calculation of aggregate size? How I can calculate the size distribution of aggregates or oligomers.. -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] how to change ps x axis format to ns in gyrate.xvg

On 5/5/19 10:20 AM, Ladan Mafakhe wrote: Hello I used below command gyrate to made gyrate.xvg file gmx gyrate -s md_0_1.tpr -f md_0_1_noPBC.xtc -o gyrate.xvg The gyrate.xvg file was generated ps time scale but I want to generate this curve on ns time scale . so I used below command

Re: [gmx-users] H bond dynamics, remove thermostat?

On 5/3/19 10:20 AM, Neena Susan Eappen wrote: Hello gromacs users, I am interested in studying the H-bond dynamics of my protein. Do you recommend to turn off thermostat for production run? Why is an NVE ensemble more appropriate for what you're doing than NVT or NPT? -Justin --

Re: [gmx-users] Membrane-protein Simulation

Please don't reply to the whole digest. On 5/6/19 6:47 AM, Sankaran SV . wrote: @email on Membrane protein Simulation: https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2019-May/125180.html Dear Najamuddin Memon Thanks for your reply. I am a little confused here. Why is the

[gmx-users] Pot'l energy difference between runs

Dear users, I've run a water membrane model through minimization, nvt, and npt with pressure coupling = surface tension with compression 4.5e-5 4 0 and with 4.5e-5 4.5e-5. I wanted to increase the box size in the z direction to created an air ( really vacuum ) interface. The membrane is in the

Re: [gmx-users] gmx mdrun with gpu

Share a log file please so we can see the hardware detected, command line options, etc. -- Szilárd On Sun, May 5, 2019 at 3:53 AM Maryam wrote: > Hello Reza > Yes I complied it with GPU and the version of CUDA is 9.1. Any suggestions? > Thanks. > > On Sat., May 4, 2019, 1:45 a.m. Reza