[gmx-users] Avg. Volume in NPT by Small Coupling Time
johnny.lu128 at gmail.com
Thu Nov 6 17:12:24 CET 2014
Assume sampling is sufficient in all stages of simulations.
Will the berendsen barostat with this coupling constant give both the
correct average volume and correct average pressure? (despite the
distribution is not canonical)
Will that average pressure change when I switch to NVT ensemble?
Can I switch to NVT directly (without doing a NPT with PR barostat) for a
while, and then finally go to NVE production run?
(a nature communication paper did that, but didn't report the barostat
coupling constant they used in the NPT simulation.)
On Thu, Nov 6, 2014 at 10:51 AM, Mark Abraham <mark.j.abraham at gmail.com>
> I think that's fine for rapidly forcing the volume to be close to the right
> equilibrium value, with low fluctuations. Then switch to gentler NPT (or
> constant-volume) for making a proper observation of the pressure.
> On Thu, Nov 6, 2014 at 4:44 PM, Johnny Lu <johnny.lu128 at gmail.com> wrote:
> > Hi.
> > How to get an accurate average volume for a system, such that the
> > will be at 1 bar in a subsequent NVT run using this average volume?
> > Is it ok to use Berendsen barostat with a very small time constant (0.2
> > ?
> > (At first I picked 0.1ps, gromacs 4.6.7 told me to use at least 0.2 ps).
> > I was hoping that a smaller time constant would allow the simulation to
> > sample the volume more frequently and Berendsen barostat would help the
> > system to converge to the correct average volume faster.
> > What are the possible draw backs?
> > So far (2 ns), I see that the pressure fluctuation is smaller than a PR
> > barostat.
> > It seems to be fine to use Berendsen barostat for this purpose ( [
> > ]
> > )
> > Thank you again.
> > --
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