[gmx-users] simulation continuation - gen-vel = yes

John Whittaker johnwhittake at zedat.fu-berlin.de
Thu Jun 13 13:04:00 CEST 2019

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

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

- John

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