Hi, gen-vel is interpreted by grompp, never mdrun.
Mark On Thu., 13 Jun. 2019, 13:04 John Whittaker, < [email protected]> wrote: > 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 [email protected]. > -- 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 [email protected].
