[gmx-users] Instantaneous velocities of a group of atoms

Frederic Leroy frederic.leroy at urv.net
Fri Jul 1 03:38:11 CEST 2005

Dear Gromacs users,

I am performing calculations of a solvated molecule. I would like to 
obtain the instantaneous velocities of each atom of the solvated 
molecule. I am not interested in those of the solvent.
The problem is that if I use the traj.trr file, the solvent contribution 
is written in this file and its size becomes huge because of the number 
of solvent molecule. And if I use the traj.xtc file I can obtain 
informations about the precise group of atoms I'm interested in but 
these informations are only positions, and not velocities... Anyway, I 
can recalculate the velocities from positions but the precision I obtain 
for positions from the traj.xtc file is too low and computed velocities 
are not reliable. Moreover, I don't see any difference on the precision 
on positions written in an .xvg file by g_traj_d if I use a value of 
1000 or 1.0e+8 for xtc_precision in the .mdp file.

So my questions are : is it possible to write only the velocities of a 
group of atoms in a traj.trr file?
Or, how can I get more precise positions in an ascii format from the 
traj.xtc file?

Thanking you by advance.
Frédéric, Tarragona U., Spain.

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