[gmx-users] Vacuum disappear after NPT equilibration?

Guangwei Jiang guangwei.jiang at qmul.ac.uk
Sat Jan 18 15:02:11 CET 2014

Thanks, Justin!

But I am still puzzled about the way to do equilibration without NPT.

How can we realize the equilibration for a reasonable density in such vacuum scheme?

Forgive me the stupid question. Thanks very much!


From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Justin Lemkul <jalemkul at vt.edu>
Sent: Friday, January 17, 2014 8:59 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Vacuum disappear after NPT equilibration?

On 1/17/14, 2:13 PM, Guangwei Jiang wrote:
> Thanks very much, Justin!
> Yes, in NVT equilibration, the box size does not change. But can I skip the NPT equilibration process to the MD modulation directly?

You should equilibrate the system and then collect data under the ensemble that
you need to model.  There is no one, single, universal way to equilibrate a system.

> Besides, in NPT equilibration, the semiisotropic pressure coupling is used. Does that mean the box in z-axis is already incompressible? But we can see the box in z-axis is still shrinking.

No, that means the scaling of box vectors in x and y are uniform and z is
independent.  You can, in theory, make the z direction fixed by setting the
compressibility along z to zero.



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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