AMBER Archive (2009)

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

From: Richard Owczarzy (rowczarzy_at_idtdna.com)
Date: Fri Dec 11 2009 - 18:19:31 CST

Long answer: The amount of solvent may depend on type of simulations. My
thinking is that you do not want the molecule to interact with its
periodic image and create artifacts. Electrostatic interactions are the
longest interactions and they are especially significant in DNA
molecules. Therefore, the box should be big enough to embody the
molecule and at least half of the range of electrostatic interactions
from the surface of the molecule. The box should be big enough in all
directions because DNA molecule will rotate during long simulations. In
other words, rectangular box with much different length and height is
usually not optimal. If you run single stranded DNAs and you start from
compact structure, consider that the molecule may relax and expand
significantly.

Richard

-----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: 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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