Thank you very much for answering my questions.
At that time, I worried that the average pressure of the NVT production
simulation would be far from 1 bar because the volume of the NVT simulation
is not near the average volume. Mostly, I just want the NPT equilibration
to give a reliable average for the NVT production simulation.
Not sure if the first NPT equilibration (100ns, normal coupling constant
for barostat) can give a reliable average volume for a protein with ~100
amino acid residues.
I didn't find many papers with a large coupling constant for barostat. I
guess I will rerun the simulation for 5 days if there is time and forget
about getting the right average pressure.
I didn't know that the average compressibility (or other thermodynamic
averages) would be less correct if the Berendsen barostat has a large
coupling constant... I didn't read a lot about barostats.
Does the compressibility have the wrong average or wrong distribution? Is
it a problem of sampling or it is plainly wrong even in theory?
On Sun, Oct 1, 2017 at 11:37 PM, Jason Swails <jason.swails.gmail.com>
wrote:
> On Thu, Sep 28, 2017 at 9:14 PM, R zu <rzu512.gmail.com> wrote:
>
> > Hi.
> >
> > After minimization and a short heating, I try to run NPT equilibration
> > before running NVT production simulation.
> >
> > The volume of the last frame of the equilibration isn't close to the
> > average volume.
> > I worry that the NVT production would have a high pressure like 100 bar.
> >
>
> Instantaneous pressures are rather meaningless in MD simulations.
> Pressure is a macroscopic quantity, which means you need to look at the
> ensemble (average) pressure over an entire (ergodic) simulation. Given the
> very high isothermal compressibility of water, tiny volume fluctuations
> yield correspondingly huge pressure fluctuations.
>
> What this means is that seeing an instantaneous pressure near 100 bar (or
> -100 bar) is perfectly normal for condensed phase MD simulations. Using a
> large coupling constant is actually worse than using a short one for the
> Berendsen barostat, as a short coupling constant typically yields computed
> compressibilities closer to experimental values (even better is to use the
> Monte Carlo barostat, which samples from the correct isothermal-isobaric
> ensemble). Said perhaps more clearly -- shorter coupling constants yields
> more physically realistic pressure-dependent behavior.
>
> Berendsen thermodynamic regulation (either a thermostat or barostat)
> artificially reduces fluctuations compared to what is expected in the true
> ensemble. The smaller the coupling constant for the barostat, the larger
> the fluctuations become (this should make sense if you think about the fact
> that you need larger changes to respond to deviations from the target value
> in a shorter amount of time). Therefore, shorter coupling constants will
> compensate for the artificial reduction in fluctuations induced by the
> Berendsen approach.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
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Received on Wed Oct 04 2017 - 09:00:04 PDT
