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

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

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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