[gmx-users] Velocity as a function of distance Z

[Mark Abraham]

Hi,


On Tue, Feb 28, 2017 at 11:55 AM Kamps, M. <m.kamps at 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
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