AMBER Archive (2005)

Subject: Re: AMBER: Energy Comparisons

From: Wei Chen (gtg553p_at_mail.gatech.edu)
Date: Wed Aug 17 2005 - 17:24:08 CDT


Hi,

I think it is better for you to compare free energy.

Wei Chen

ÒýÓÃ Kara Di Giorgio <kdigiorgio_at_sbcglobal.net>:

> I'm trying to compare md runs of several drugs bound to a short DNA
> strand. In terms of comparing energies, which is best to use ETOT,
> EPTOT or some other parameter? The drugs generally differ by a
> methylene group.
>
> Thank you,
>
> Kara Di Giorgio
> University of the Pacific
>
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