Re: AMBER: GB dynamics

From: David A. Case <case.scripps.edu>
Date: Fri, 1 Apr 2005 08:16:46 -0800

On Fri, Apr 01, 2005, mathew k varghese wrote:
>
> I am running an MD simulation of a bulged RNA with
> implicit solvent(igb=1).When I neutralized the system
> with Na+ ions....

We generally do not recommend that use use explicit ions with GB models;
or at least, there is very little experience about whether this would work or
not. Consider setting the salt concentration variable as an alternative.

If you do wish to try out explicit ions, you should treat this as a research
project, going into new territory.

....good luck...dac 
-- 
==================================================================
David A. Case                     |  e-mail:      case.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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Received on Fri Apr 01 2005 - 17:53:01 PST
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