[gmx-users] Equilibration

[Justin Lemkul]

On 2/28/18 6:38 AM, Amin Rouy wrote:
> Thanks Justin, however,
>
>
>         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).
>
> Yes, but if a system goes to equilibrium in NVT, pressure should be 
> fluctuating around a stable value.  For any system with defined N, T, 
> V there should be one value for pressure, is not it?

Pressure fluctuates pretty wildly, and in NVT there is no barostat 
regulating it, so no, you should not expect to see any sort of stable 
value in this quantity.

-Justin

>         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
>
>     -- 
>     ==================================================
>
>     Justin A. Lemkul, Ph.D.
>     Assistant Professor
>     Virginia Tech Department of Biochemistry
>
>     303 Engel Hall
>     340 West Campus Dr.
>     Blacksburg, VA 24061
>
>     jalemkul at vt.edu <mailto:jalemkul at vt.edu> | (540) 231-3129
>     <tel:%28540%29%20231-3129>
>     http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>     <http://www.biochem.vt.edu/people/faculty/JustinLemkul.html>
>
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-- 
==================================================

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

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==================================================