[gmx-users] Question regarding the concept of ensembles

Justin Lemkul jalemkul at vt.edu
Mon Feb 20 14:19:47 CET 2017

On 2/20/17 8:14 AM, ali.khourshaei71 at student.sharif.edu wrote:
> Dear Justin,
> Thanks very much for your response. I have one more question regarding
> your answer to Question 4. Although A long tau-p means the box vector
> can change very slowly in response to the computed pressure, if for
> instance I choose tau-p= 100000 for my lipid bilayer system, I will
> notice that the length of simulation box won't change at all. So, Can I
> conclude that if I choose a very very large tau-p, it will be equivalent
> to compressibility =0 ? I think based on the formulation of berendsen
> pressure coupling I can claim that. Can't I?

It's not equivalent, though it may be an approximation.  If your simulation is 
longer than 100 ns, though, you're going to see a response from the barostat 
that will change the box vector.  If you want a given dimension to be constant, 
the simplest and most intuitive thing to do is simply set its compressibility to 
zero rather than trying to play lots of tricks.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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