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

[Ali Sinan Saglam]

Hi Mark,

Thank you for the suggestion, that's what I needed to know!

Best,
Ali Sinan Saglam


On Fri, Aug 30, 2013 at 3:51 AM, Mark Abraham <mark.j.abraham at gmail.com>wrote:

> >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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