[gmx-users] Equilibration

[Justin Lemkul]

On 2/27/18 10:05 AM, Amin Rouy wrote:
> Hi,
>
> I run a simulation of a solute in water. I have 2 question please:
>
> 1- After NVT equilibrium, I see that all quantities like energies and
> temperature become stable, except pressure. Should I continue till pressure
> also goes stable? or can I move forward and do it in production run?

Pressure isn't a conserved quantity in NVT. It is in NPT (hence the P).

> 2- My interest production run is NVT, should I run 2th-step-equilibrium
> with NPT also? or only NVT equilibration is enough?

Model whatever conditions are relevant to you; even with NVT, you may 
want to simulate at a fixed density, which requires NPT equilibration to 
stabilize the pressure/density and then continue with NVT. Rarely is the 
initial configuration ideal.

-Justin

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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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