I am sorry about the point of Berendsen barostat.
One comparison of the barostats says it doesn't give the correct average.
http://pubs.acs.org/doi/pdf/10.1021/acs.jctc.5b00748
The reference 5 and 6 link to the the flying ice cube problem, and
collective motion artifacts.
I guess the problem is that it would take forever to get the correct
average?
On Wed, Oct 4, 2017 at 11:49 AM, R zu <rzu512.gmail.com> wrote:
> 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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>>
>
>
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Received on Wed Oct 04 2017 - 09:30:04 PDT
