[gmx-users] Vacuum disappear after NPT equilibration?

Justin Lemkul jalemkul at vt.edu
Fri Jan 17 22:01:07 CET 2014

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


More information about the gromacs.org_gmx-users mailing list