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

Mark Abraham mark.j.abraham at gmail.com
Mon Feb 27 21:10:40 CET 2017


A group whose composition is defined geometrically over time requires
constructing a dynamic selection, which is done with gmx select.
Unfortunately that currently means writing a script to loop over frames,
calling gmx select to make a suitable index file, then here e.g. gmx traj.
Do check out gmx traj -h for useful options there.


On Mon, 27 Feb 2017 13:11 Kamps, M. <m.kamps at student.rug.nl> wrote:

Dear gmx-users,

I have several simulations regarding atoms flowing between two gold
surfaces. The flow of the liquid molecules show a distinct Poiseuille
flow, which was expected.
I am now interested in extracting the velocities of these liquid
molecules (total of around 30000 atoms, around 700 molecules).

I am interested in the (average) velocity, as a function of the height
Z. Is this possible in any way?

If I take for example the command gmx traj ... -av, I will get the
average velocity of all atoms, however I cannot tell which atom is
placed where. Furthermore, is it possible to get the average
velocities per molecule instead of atoms, for instance via gmx traj?

Thanks in advance.

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