AMBER Archive (2005)

Subject: Re: AMBER: GB dynamics

From: David A. Case (case_at_scripps.edu)
Date: Fri Apr 01 2005 - 10:16:46 CST


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_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 ================================================================== ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to amber_at_scripps.edu To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu