Hi all, I have a simple question that I hope someone can answer.
When I began my simulation, my .mdp file had "gen-vel = yes" in order to generate some initial velocities. My next simulation was a continuation of the first (I am setting nsteps = -1 and running mdrun with the flag -maxh in order to run as long as possible on a cluster). Now, for my second simulation, I am issuing a command like: gmx mdrun -s ../previous_sim/topol.tpr -cpi ../previous_sim/state.cpt (I realize now I should probably only use the -cpi flag, as the -s is redundant) Since I am passing mdrun a .tpr file that has "gen-vel = yes", does this mean that I am generating new velocities in this simulation that is supposed to be a continuation? Or does the generation of velocities *only* happen during the .tpr generation (grompp) and mdrun ignores that part and just continues from the state specified by state.cpt? I'm just worried I've been introducing a discontinuity in the temperature and not simulating in equilibrium. Please let me know if I can clear anything up, thanks in advance for any information. - John -- 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.
