[gmx-users] Vacuum disappear after NPT equilibration?

[Guangwei Jiang]

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

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Justin A. Lemkul, Ph.D.
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