Re: [gmx-users] Energy drift

= no ;gen_temp = 293.15 ;gen_seed = -1 _ Xiaobin Cao Dept of Geology Geophysics E235, Howe-Russell Geosciences Complex, Louisiana State University, Baton Rouge, LA 70803, U.S.A

Re: [gmx-users] Energy drift

Thank you, Mark. I am following this paper: Mutual diffusion coefficients of heptane isomers in nitrogen: A molecular dynamics study (JCP, 2011). They use flexible model, so do I (please check my top and mdp files). Actually I already checked the time step of 0.5fs, and it does not work. Belows

Re: [gmx-users] Energy drift

Hi, Mark. I tested my system today with NVE and time step =1fs and 0.5fs. The drift still exists. I didn't test the system by double precision GROMACS yet. Thank you. _ Xiaobin Cao Dept of Geology Geophysics E235, Howe-Russell Geosciences Complex

Re: [gmx-users] Energy drift

a step is small enough to suppress the drift? Mark _ Xiaobin Cao Dept of Geology Geophysics E235, Howe-Russell Geosciences Complex, Louisiana State University, Baton Rouge, LA 70803, U.S.A. -- Gromacs Users mailing list * Please search the archive

Re: [gmx-users] Energy drift

Thank you, Mark. I doubt the potential model right now. But I didn't find a good model for N2 gas. Can you give me some suggestions? Can I use COMPASS potential in GROMACS? Thanks -- Gromacs Users mailing list * Please search the archive at

[gmx-users] How can I select a group number automatically

Hi Gromacs users, When I do msd analysis (g_msd), there is a promotion to select a group number. I am wondering how can I select a number using a script. So the computer can do analysis automatically. Thank you. _ Xiaobin Cao Dept of Geology

Re: [gmx-users] How can I select a group number automatically

Thank you, Erik and Chandan. They all work well. They will save me a lot of time. _ Xiaobin Cao Dept of Geology Geophysics E235, Howe-Russell Geosciences Complex, Louisiana State University, Baton Rouge, LA 70803, U.S.A. Or redirected input: g_msd

Re: [gmx-users] How can I select a group number automatically

Yes. Thank you, Mark. _ Xiaobin Cao Dept of Geology Geophysics E235, Howe-Russell Geosciences Complex, Louisiana State University, Baton Rouge, LA 70803, U.S.A. And there are even more options at http

[gmx-users] run g-msd using more than one core

Dear GROMACS users, I want to analyze the diffusion coefficient using g_msd. Can I run this command using more than one core, and how? I tried MPI version, but I can only use one core even I applied 16 cores on a supercomputer. Thanks _ Xiaobin Cao