[gmx-users] Saving velocities of one atom at every timestep

[Andrew DeYoung]

Hi,

I have a rather large system (~10,000 atoms) -- at least, I consider it
rather large since I'm using a cluster, not a supercomputer.  

I want to save the velocities of a single atom of interest at every
timestep, so that I can use g_velacc to calculate the velocity
autocorrelation function.  I only care about the single atom of interest;
I'm not interested in the coordinates, velocities, and forces of the other
many thousands of atoms in my system.

In other words, I have enough disk space to save the velocities of the atom
of interest for every timestep for, say, several millions of steps.  But I
don't have enough space to save the velocities of all 10,000 atoms for every
timestep for several millions of steps.

I'm running Gromacs version 4.5.5.  Setting nstxtcout = 1 allows one to save
the coordinates of the groups specified in xtc-grps to the xtc trajectory.
Is there any built-in way to save velocities -- rather than coordinates --
for only a specified group (a single atom, in this situation)?

Or would it be possible to use the xtc to save the coordinates of the atom
of interest at every timestep, and then somehow convert these coordinates to
velocities so that I can use g_velacc?  I'm using the leapfrog integrator
(integrator = md).

Thanks so much for your time!

Andrew DeYoung
Carnegie Mellon University