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

Justin A. Lemkul jalemkul at vt.edu
Sat May 16 00:32:04 CEST 2009

bohumir wrote:
> Dear GROMACS Masters,
> is there a trick to obtain coordinates and velocities of center of
> mass of each water molecule?

Have a look at g_traj, although to analyze each molecule separately could take 
many iterations with specific index groups.


> 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?
> Thanks for a great tool,
> -Bohumir
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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