[gmx-users] gromacs charges

David van der Spoel spoel at xray.bmc.uu.se
Mon Sep 30 08:51:18 CEST 2002

On Fri, 2002-09-27 at 17:15, quantix1 at gmx.de wrote:
> Dear Gromacs-Users,
> I am completely new to Gromacs. Let's say, I'm still thinking about using
> it. My first question is, how charges for non-standard amino acids or other
> molecules are usually derived for the force field in Gromacs. Is there a
> procedure which is considered to be standard and gives the most 
> consistent results (like the HF/6-31G -> RESP for AMBER) ?
> This should be enough before the weekend. Thanks in advance,

In the GROMOS force fields there are no standard recipes, except "by
analogy", which means that we presume that e.g. alcohol groups will have
the same charges in methanol and ethanol. GROMACS also supports OPLS
which is a bit better in systematically deriving parameters. But here
you have to find some literature to check how...
> Uwe
> -- 
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Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel

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