Quoting bohumir <[email protected]>:
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.
--
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Jussi Lehtola, FM, Tohtorikoulutettava
Fysiikan laitos, Helsingin Yliopisto
[email protected], p. 191 50632
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Mr. Jussi Lehtola, M. Sc., Doctoral Student
Department of Physics, University of Helsinki, Finland
[email protected]
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