AMBER Archive (2002)

Subject: Density during equilibration (sander)

From: Pratul Agarwal (pratulka_at_rocketmail.com)
Date: Tue Sep 17 2002 - 11:56:10 CDT

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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