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

[John Whittaker]

Thank you, Mark. That makes me feel better.

- John

> 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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