[gmx-users] Instantaneous velocities of a group of atoms
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
Thanking you by advance.
Frédéric, Tarragona U., Spain.
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