[gmx-users] Re: g_msd additional information

Hi Justin, thank you so far. Now I got some more specific questions regarding g_msd I got my trajectory from 0-30ns. So far it should to be "correct". I was analyzing this trajectory with g_msd and the following command: g_msd -f mdrun.xtc -s mdrun.tpr -nice 0 -b 0 -e 3 -beginfit 15000 -endf

[gmx-users] Virtual sites LJ/mass

Dear Gromacs-Experts, for my simulations of pure hexane (united atom model) I would like to separate the mass and the interaction parameters of the CH3. So far I tried several different setups by using virtual sites but none of them is working. I hope somebody can help. Here is some background in

[gmx-users] g_msd additional information

Dear GROMACS Experts, I am using GROMACS to simulate the self-diffusion coefficient of a wide range of pure systems (e.g. alkanes). Unfortunately the information given in the manual regarding g_msd and its exact calculation in GROMACS is insufficient for me. Does somebody got some idea of papers

[gmx-users] Re: NPT with md-vv + Nose-Hoover + Parinello-Rehman

Hi Tarak, I have had the same problem. As far as I know, it is not possible to use Nose-Hoover + Parrinello-Rahman in combination with the md-vv integrator. I am using md (leap-frog) in combination with Nose-Hoover + Parrinello-Rahman, this is working fine. I guess it would be great to get a con