[gmx-users] Saving velocities

Mark Abraham mark.abraham at anu.edu.au
Sun Aug 29 13:43:31 CEST 2010

----- Original Message -----
From: pojeda at icp.uni-stuttgart.de
Date: Saturday, August 28, 2010 2:11
Subject: [gmx-users] Saving velocities
To: gmx-users at gromacs.org

> Hi,
> Does anybody knows how to save the velocities of a group of particles
> every N time steps without having to write the .trr file for the whole
> system? I mean my system has two kinds of molecules say A and 
> water what
> I want is to save the velocities for the atoms in the molecule A
> every certain number of steps. The .trr file seems to be very big.
> Therefore I just want to write the velocities of the molecule A which
> is small.

It can't be done inside mdrun. The best you can do is use trjconv on the full .trr to select only the desired group, having defined a suitable index group first. Then you can discard the full .trr.


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