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 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.