thanks for the info!
On Thu, Aug 6, 2015 at 1:03 AM, Jason Swails <jason.swails.gmail.com> wrote:
> On Wed, Aug 5, 2015 at 7:34 PM, Adrian Roitberg <roitberg.ufl.edu> wrote:
>
> > Unless I am reading this wrongly, you did
> >
> > 2 fs dt, nstlim=2000000 --> 4 ns/10.6 hours
> > 4fs dt , nstlim=2000000 --> 8 ns/11.5 hours
> >
> > So, basically in the same wallclock time, you DOUBLED the simulation
> > time. That is exactly what is supposed to happen, right ?
> >
>
> ​Just to add in a little bit here -- you would naively expect the wallclock
> time to stay the same if all you're changing is the time step. But keep in
> mind that with a 4 fs timestep, particles move farther (about twice as far)
> as with a 2 fs timestep. As a result, particles diffuse farther *per
> timestep*, meaning that the pairlist will need to be rebuilt significantly
> more often. Since pairlist builds are fairly expensive, this will account
> for the extra ~10% slowdown in the apparent per-timestep efficiency.
>
> But as Adrian pointed out, this 10% slowdown is more than countered by
> doubling the timestep, such that the total ns/day is slightly less than
> double the ns/day for a 2 fs timestep.
>
> All the best,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Wed Aug 05 2015 - 17:30:04 PDT
