Re: Water bubbles in NVT equilibration dynamics

From: Ana Celia Vila Verde (
Date: Mon Aug 27 2012 - 09:23:51 CDT

Dear Mariana,

After minimization, one should always run an NPT equilibration where
only the water atoms are allowed to move. Only when the average volume
of this simulation is approximately constant can you proceed with a
further NVT equilibration, and then any runs you want. Note that the
starting configuration for the NVT equilibration should be obtained
from the NPT run by: 1- calculating the average volume of the NPT run
once it has stopped drifting; 2- finding a saved dcd frame where the
instantaneous volume is very close to the average one.

I hope this helps.


On 8/25/12 1:52 AM, Mariana Graterol wrote:
> Hello,
> I want to equilibrate my protein in a water box, using PBC, ions, and
> everything to set up my molecular dynamics.
> I noticed water grouping during my equilibration dynamics NVT. (It
> looked like many bubbles -spherical spaces without water molecules- in
> my box); I guess that something it's wrong with pressure/volume since
> I didn't carry on control pressure before i started the NVT run of
> production.
> I had understood that a protocol it was minimize-heating-equilibrate
> temperature (NVT)- and finally I will do a production run to evaluate
> certain residues in my system as time evolves.
> Is it recommended or is it necessary first equilibrate my system at
> constant pressure and temp. NPT, before I run NVT equilibration?
> and how NAMD controls density in a water box? because maybe it was a
> drift in density?
> Thank you in advance for any help..
> Lic. Mariana Graterol
> PhD student. Universidad Central de Venezuela
> --
> * mari *

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