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

[Kamps, M.]

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.
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.

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?

Mark