Re: [gmx-users] Energy drift combining tabulated potentials and group cut-off.

Hello, Thank you very much for your thoughtfull response. The structural properties seem to be represented correctly so I guess it should work. I know that drifts are something we must live with but since it appeared when changing the system to a tabulated potential+a group cutoff I was not sure

[gmx-users] Calculating hydrogen bonds along the length of the Bilayer

Hi Experts,How can we calculate hydrogen bonds as a function of distance from the Bilayer centre.ThanksYogi -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Error while running perl distances.pl

Script assumes that variable $distance is the second row separated by space in the file dist{number}.xvg which appears after execution of system call gmx distance -s md_pull.tpr -f conf${i}.gro -n index.ndx -oall dist${i}.xvg -select \'com of group \"lig\" plus com of group \"protein\"\'I just

Re: [gmx-users] Regarding position restraining in nvt.mdp and npt.mdp files

Hi, See http://www.gromacs.org/Documentation/How-tos/Position_Restraints. And do manage the spelling of the abbreviation correctly! Mark On Mon, 4 Sep 2017 06:27 Dilip H N wrote: > Hello, > I am running a peptide simulation, i have done an energy minimization , now