[gmx-users] RE: average pressure of a system

[Justin Lemkul]

On 9/11/13 12:12 AM, Dwey Kauffman wrote:
>> True, but thermostats allow temperatures to oscillate on the order of a few
> K,
>> and that doesn't happen on the macroscopic level either.  Hence the small
>> disconnect between a system that has thousands of atoms and one that has
>> millions or trillions.  Pressure fluctuations decrease on the order of
> sqrt(N),
>> so the system size itself is a determining factor for the pressure
> fluctuations.
>>   As previous discussions have rightly concluded, pressure is a somewhat
>> ill-defined quantity in molecular systems like these.
>
> Dose it also imply that it is not a good idea to study the relationship
> between dimer (multimer) dissociation and  macroscopic pressure in this case
> ?  (due to the ill defined pressure).
>

I would simply think it would be very hard to draw any meaningful conclusions if 
they depend on a microscopic quantity that varies so strongly.

> It is hard to be justified if I assign a set of various ref_p= 0.7, 0.8,
> 0.9, 1.0, 1.1, 1.2 ...., perform independent simulations, and then obtain
> outcomes of targeted quantities for comparison.
>

As with the original issue, I would find it hard to believe that any of the 
differences observed in such a setup would be meaningful.  Is 0.7 ± 100 actually 
different from 1.2 ± 100?

>>
>> You could try altering tau_p, but I doubt there is any value in doing so.
>
> I would give it a try.
>

This will really only change the relaxation time.  Smaller values of tau_p may 
improve the average slightly, but may also (more likely) lead to instability, 
especially with Parrinello-Rahman.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
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jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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