[gmx-users] A question about velocity rescaling thermostat and velocity verlet integrator

[Mark Abraham]

>From memory, the Bussi thermostat does take its seed from ld-seed. You
can see this yourself by observing that mdrun -reprod with ld-seed set
to some value of your choice is reproducible by itself and different
from that of a different ld-seed.

Mark

On Thu, Aug 29, 2013 at 9:15 PM, Ali Sinan Saglam
<asinansaglam at gmail.com> wrote:
> Hi,
>
> I was planning to use the velocity verlet ingetrator (md-vv) with velocity
> rescaling thermostat (tcoupl = v-rescale). I know that velocity rescaling
> thermostat is a stochastic thermostat and uses a random seed and generally
> with the stochastic thermostats one would use the sd integrator that uses
> ld-seed = -1 option for a random seed.
>
> I was just wondering if one uses the velocity verlet integrator with a
> stochastic thermostat does the ld-seed option work as it does with the sd
>  (or bd) integrator?  (the manual currently doesn't say anything about this
> http://manual.gromacs.org/online/mdp_opt.html#run)
>
> Best,
> Ali Sinan Saglam
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