[gmx-users] Question regarding the concept of ensembles

[Justin Lemkul]

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 
in place?

> 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
> amount?
>

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

-- 
==================================================

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
http://mackerell.umaryland.edu/~jalemkul

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