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

[Mark Abraham]

Hi,

gen-vel is interpreted by grompp, never mdrun.

Mark

On Thu., 13 Jun. 2019, 13:04 John Whittaker, <
johnwhittake at zedat.fu-berlin.de> 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
>
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