[gmx-users] Question regarding the concept of ensembles
jalemkul at vt.edu
Mon Feb 20 14:06:41 CET 2017
On 2/20/17 7:59 AM, ali.khourshaei71 at student.sharif.edu wrote:
> Dear Gromacs users,
> I have 4 question regarding the concept of the ensemble.
> 1. In NVT ensemble the length of the simulation box remains constant in
> x,y and z direction. Does it mean that all the atoms within the system
> become freeze and have no movement?
No. Do an NVT simulation and watch the trajectory. Does everything stay fixed
> 2. In NPT ensemble if I choose compressibility = 0 in one specific
> direction, does the length of the simulation box only becomes constant
> in that direction or all the atoms become freeze in that direction too?
Again, there's no freezing due to an ensemble. If you define zero
compressibility in some direction, then the box vector along that axis is fixed.
> 3. Is NVT ensemble equivalent to NPT ensemble with negligible
> compressibility in x,y, and z direction?
Strictly speaking, it means zero compressibility in all dimensions.
> 4. To constant the thickness of the simulation box, is there any
> difference if I choose compressibility = 0 or choose tau-p as very high
Yes, there is a difference. Zero compressibility means the box vector will not
change. A long tau-p means the box vector can change very slowly in response to
the computed pressure (i.e. slow barostat response time).
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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