AMBER Archive (2009)

Subject: Re: FW: Solvent/solute ratio? Re: [AMBER] how to add desired numberof water

From: Hopkins, Robert (hopkins_at_uhcl.edu)
Date: Fri Dec 11 2009 - 16:24:02 CST

Thanks very much for your prompt reply and suggestion!

Bob Hopkins

-----Original Message-----
From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On
Behalf Of Bill Ross
Sent: Friday, December 11, 2009 4:20 PM
To: amber_at_ambermd.org
Subject: [Possible Spam: 10%] Re: FW: Solvent/solute ratio? Re: [AMBER]
how to add desired numberof water

> How *does* one estimate an appropriate amount
> of solvent for a given solute molecule in a MD simulation in
explicit=20
> solvent?

My sense of it is, you want more than your cutoff, by some margin
to allow for box shrinkage during equilibration. For nucleic acids,
I have used 10A water (before adding ions) with 8A cutoff.

Bill

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