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

bohumir bohumir at gmail.com
Sat May 16 00:07:21 CEST 2009

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?

Thanks for a great tool,

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