AMBER Archive (2009)

Subject: Re: [AMBER] Irregularity in box during md

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Tue Feb 10 2009 - 11:24:12 CST


> constant volume molecular dynamics
> ...
> distorted distribution of water molecules around the peptide.

Vdw voids are created by water placement. They aggregate with
constant volume dynamics. Constant pressure dynamics are required
to equilibrate to normal density.

Bill

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