Re: Water bubbles in NVT equilibration dynamics

From: Jeffrey Potoff (
Date: Mon Aug 27 2012 - 10:00:39 CDT

One gets "bubbles" in these cases because they don't have enough water
in the system to give them a correct density of approximate;y 1 g/cm^3.
Running NPT may help, but it depends on how wrong one's original
estimate was for the number of required water molecules. If one is too
far off, they will have to deal with the infamous "patch grid error".

On 8/27/2012 10:23 AM, Ana Celia Vila Verde wrote:
> 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.
> Ana
> 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 *

Jeffrey J. Potoff
Associate Professor  and Director of Early Engineering Programs
Department of Chemical Engineering and Materials Science
Wayne State University			5050 Anthony Wayne Dr
Detroit, MI 48202  	                TEL: (313) 577-9357

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