AMBER Archive (2003)

Subject: Re: AMBER: solvatebox-solvateshell

From: David A. Case (case_at_scripps.edu)
Date: Sat Sep 06 2003 - 14:56:39 CDT

On Sat, Sep 06, 2003, Majid moghaddam wrote:

> I prefer to use solvateshell instead of solvatebox to
> decrease the time, but I am not sure if it is really
> better and I don't know what I should do for periodic
> boundary conditions.

I don't know what time it is you want to decrease. Solvateshell creates just
a sphere of water molecules about some point. It is not very accurate, since
the polarization of waters outside the "shell" is not accounted for, and there
can be unphysical effects at the water-vacuum boundary at the edge of the
water shell.

Solvateshell cannot be used for periodic simulations; use solvateBox or
solvateOct for that purpose.

..good luck...dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |    http://www.scripps.edu/case
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