AMBER Archive (2009)

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

From: Dean Cuebas (deancuebas_at_missouristate.edu)
Date: Mon Dec 14 2009 - 20:40:25 CST

One of the most important things to check in terms of quality assurance is
that there have not been direct interactions between periodic images. Since
periodic images are identical, such interactions are unphysical
self-interactions. Imagine that a protein with a dipole would have direct
interactions. Then the attraction between the two ends of the same molecule
over the periodic boundary would affect and invalidate the results relating
to the native behaviour of the protein.

Not only direct interactions are of concern, but indirect effects, mediated
through the water can also pose a problem. For instance, the protein can
cause water ordering in the first four shells of water. That corresponds to
about 10 A. Ideally, the minimal distance should therefore not be less than
20 A between images.

(Taken from http://nmr.chem.uu.nl/%7Etsjerk/course/molmod/analysis.html)

Hope this helps,

Dr. C 

-- 
Dr. Dean Cuebas, Associate Prof of Chemistry
deancuebas_at_missouristate.edu, Ph 417-836-8567 FAX 417-836-5507
Dept. of Chemistry, Missouri State University
Springfield, Missouri 65897

> From: "Hopkins, Robert" <hopkins_at_uhcl.edu>
> Reply-To: AMBER Mailing List <amber_at_ambermd.org>
> Date: Fri, 11 Dec 2009 16:24:02 -0600
> To: AMBER Mailing List <amber_at_ambermd.org>
> Subject: Re: FW: Solvent/solute ratio? Re: [AMBER] how to add desired numberof
> water
> 
> 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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