Re: Density during equilibration (sander)

From: Pratul Agarwal <>
Date: Thu 26 Sep 2002 07:09:02 -0700 (PDT)

This is mainly for the archives.

I found the source of the problem and a fix. The problem was with
performing the constant pressure MD with restraints on the solute
atoms. To get the final density closer to 1.0 g/cc, I decided to
perform an additional small time period constant pressure MD after all
the steps of equilibration (when all restraints on the solute atoms
have been gradually removed).

--- Pratul Agarwal <> wrote:
> The density of my simulation box (protein in TIP3P box) stabilizes
> around 0.90-0.94 during NPT simulation and does not reach close to
> 1.0.
> (I have tried different values of taup 0.2-1.0ps and my simulation
> length is 30ps.) Has anybody seen this problem before? I would
> appreciate any comments/suggestions.
> I have tried reducing the box dimensions in the crd file (as
> suggested
> by the GIBBS tutorial), and then the density reaches 1.0 very
> quickly.
> I was wondering if I need to follow any special set of instructions
> while doing this and if by manually decreasing the box size I would
> introduce any artificial forces/changes in the system.
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Received on Thu Sep 26 2002 - 07:09:02 PDT
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