Re: [gmx-users] WG: WG: Issue with CUDA and gromacs

Hi, -- Szilárd On Mon, Mar 18, 2019 at 2:34 PM Tafelmeier, Stefanie < stefanie.tafelme...@zae-bayern.de> wrote: > Hi, > > Many thanks again. > > Regarding the tests: > - ntmpi 1 -ntomp 22 -pin on > >OK, so this suggests that your previously successful 22-thread runs did > not > turn on

Re: [gmx-users] Replica exchange MD analysis

Thank you Justin, with your valuable input I got the solution. regards RajP On Mon, Mar 25, 2019 at 11:44 PM Justin Lemkul wrote: > > > > On 3/25/19 2:22 PM, Rituraj Purohit wrote: > > Thank you Mark for the reply. In my REMD results I would like to > > observe the structure transition with

Re: [gmx-users] Replica exchange MD analysis

On 3/25/19 2:22 PM, Rituraj Purohit wrote: Thank you Mark for the reply. In my REMD results I would like to observe the structure transition with temperature given variation (I think it is most common observation). My query here is the output of REMD, It does not give .xtc file but only .edr,

Re: [gmx-users] Replica exchange MD analysis

Thank you Mark for the reply. In my REMD results I would like to observe the structure transition with temperature given variation (I think it is most common observation). My query here is the output of REMD, It does not give .xtc file but only .edr, .log and .gro even-thou I indicated -x .xtc

[gmx-users] energygrp_excl error in g_membed run

Hi there, I'm trying to embed a protein with MG and ATP into the membrane. Based on the index file with *protein_MG_ATP* as one group and *membrane_Ion_Sol* the other, I listed these two groups as energygrps in Sample.mdp (attached), and the former as freezegrps. However, this didn't allow me to

[gmx-users] (cross-)compiling mdrun independently from the rest of gromacs tools

hi guys, according to the gromacs installation instructions (i think a saw it here: http://manual.gromacs.org/documentation/2018/install-guide/index.html) it could make sense to compile gromacs mdrun independently from the other gromacs tools in order to have a cross-compiled installation

Re: [gmx-users] Replica exchange MD analysis

Hi, This is the same as for any other scientific experiment. You need to have thought about what you hope to learn and what you need to record in order to analyse the results. REMD is essentially no different here. Mark On Sun., 24 Mar. 2019, 10:51 Rituraj Purohit, wrote: > Dear Friends, > I

Re: [gmx-users] GPU error

Hi, What did you learn from the log file when it chose to use only one GPU? If your system is tiny then two won't help... Mark On Mon., 25 Mar. 2019, 11:28 RAHUL SURESH, wrote: > Hi > > I have a system with 2 8 core gold processor and 2 1080Ti card. During > mdrun, the job utilize only one

[gmx-users] GPU error

Hi I have a system with 2 8 core gold processor and 2 1080Ti card. During mdrun, the job utilize only one GPU card. Command: gmx_mpi mdrun -v -deffnm md Trying various command line I could use both the card but end up with very poor performance. command: mpirun -np 2 gmx_mpi mdrun -v -deffnm

[gmx-users] applying surface tension to a membrane bilayer

Hi, I am trying to apply a surface tension to a membrane bilayer, below is the mdp parameters I am using: pcoupl = Berendsen pcoupltype = surface-tension tau_p = 10.0 10.0 ref_p = 500 1.0 compressibility = 4.5e-5 4.5e-5