[gmx-users] Vacuum disappear after NPT equilibration?

Mark Abraham mark.j.abraham at gmail.com
Sat Jan 18 18:21:24 CET 2014

```Hi,

Why are you trying to maintain a region of vacuum while changing the
density of the rest?

Mark

On Sat, Jan 18, 2014 at 3:02 PM, Guangwei Jiang
<guangwei.jiang at qmul.ac.uk>wrote:

> 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!
>
> Regards,
> Guangwei
>
>
> ________________________________________
> 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
>
> --
> ==================================================
>
> 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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