[gmx-users] RE: average pressure of a system
jalemkul at vt.edu
Wed Sep 11 13:47:42 CEST 2013
On 9/11/13 12:12 AM, Dwey Kauffman wrote:
>> True, but thermostats allow temperatures to oscillate on the order of a few
>> 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
>> so the system size itself is a determining factor for the pressure
>> 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 A. Lemkul, Ph.D.
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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