[gmx-users] positions and velocities of COM of whole water molecules instead of those of individual atoms?

Jussi Lehtola jussi.lehtola at helsinki.fi
Sat May 16 00:18:10 CEST 2009

Quoting bohumir <bohumir at gmail.com>:
> Dear GROMACS Masters,
> is there a trick to obtain coordinates and velocities of center of
> mass of each water molecule?
> Currently, the positions and velocities of *each individual atom* of
> all water molecules are written to the "traj.trr" file.
> I would like to look at velocity profiles, but not those of individual
> water atoms - rather of the whole water molecules.
> Maybe new xdrfile-1.0.tar.gz library can help to convert "traj.trr"
> file to have molecular COM coordinates and velocities?

That, or you can use the GROMACS libraries to do the analysis. If you  
don't publish your code then it may have any license whatever; if you  
publish it then it (as GROMACS) must be licensed under GPL.

If there isn't a tool as such already available, it should be trivial to code.
Jussi Lehtola, FM, Tohtorikoulutettava
Fysiikan laitos, Helsingin Yliopisto
jussi.lehtola at helsinki.fi, p. 191 50632
Mr. Jussi Lehtola, M. Sc., Doctoral Student
Department of Physics, University of Helsinki, Finland
jussi.lehtola at helsinki.fi

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