Hi,
On Tue, Feb 28, 2017 at 11:55 AM Kamps, M. <m.ka...@student.rug.nl> wrote: > Dear Mark, > > Thanks for your reply. Correct me if i'm wrong, but your suggestion > would be to determine the position of each atom/molecule during a > frame. This process should be repeated for each frame, which is > easiest to do with a manually written (non-GROMACS) script. > Yes. For each frame, call gmx select to make whatever groups suit you in an index file, then call gmx traj with that index file to produce things related to the velocities of the atoms in those groups. > With these positions per time, gmx traj should be able to determine > the velocity of each atom/molecule? If so, I will try to figure this > out. > Sure, that's what gmx traj -ov does, which is why I suggested you look at its help text. > Furthermore, is there a way to automatically select multiple atoms as > a molecule? My simulation uses small simple polymers, is there a way > to let GROMACS calculate only the positions or velocities of the > molecules instead of the atoms? > Generally, only by making an index group for that molecule. gmx select likely does everything you can imagine, and more. http://manual.gromacs.org/documentation/2016/onlinehelp/selections.html#specifying-selections-from-command-line Mark Mark > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
