[gmx-users] Equilibration

Dallas Warren dallas.warren at monash.edu
Wed Feb 28 00:22:57 CET 2018

Not sure about with constant volume, as I don't tend to run under
those conditions, but with constant pressure the pressure will always
fluctuate quite substantially.

How big the fluctuation is depends on the size of the system, the
later the system is, the smaller the fluctuations.

Small system (6k): https://twitter.com/dr_dbw/status/968624615063937025

Larger system (300k): https://twitter.com/dr_dbw/status/968625462959210496

You really should run a component with NPT, so that the system reaches
the correct box size and pressure.  It is unlikely that the box you
set has the exact right dimensions and number of molecules to give the
correct pressure/density.
Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
When the only tool you own is a hammer, every problem begins to resemble a nail.

On 28 February 2018 at 02:05, Amin Rouy <aminrou1986 at gmail.com> 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?
> 2- My interest production run is NVT, should I run 2th-step-equilibrium
> with NPT also? or only NVT equilibration is enough?
> --
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