AMBER Archive (2007)

Subject: Re: AMBER: Box dimensions

From: David A. Case (case_at_scripps.edu)
Date: Fri Feb 16 2007 - 10:54:48 CST

On Fri, Feb 16, 2007, Akshay Patny wrote:
>
> Can anybody suggest that for NPT equilibration, should the system be
> equilibrated until volume and density becomes more or less constant?
>

Yes. Furthermore, it is typical in amber runs, especially with water as a
solvent, for the initial density to be too low (because of the way that LEaP
constructs the water box). So the equilibration process generally makes the
box smaller.

...dac

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