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.
-Justin
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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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