[gmx-users] Vacuum disappear after NPT equilibration?

[Justin Lemkul]

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.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
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jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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