AMBER Archive (2004)

Subject: Re: AMBER: extracting energy from trajector?

From: MURAT CETINKAYA (cetinkayam_at_psu.edu)
Date: Mon Nov 29 2004 - 09:31:14 CST

Actually, I wanted to calculate the energy of my system without the solvent or
the ions. So, this method seems better for me. But I do not make to wish
minimization on my ensemble of pdb files. I think I will do that by setting
minsteps=0, right?

On Mon, 29 Nov 2004 14:04:52 +0100, David Smith wrote:

> Hi Murat,
>
> I wanted to add that if this is all you want to do with this data set
> then Dr. Simmerling's suggestion of imin=5 (which I had also missed in
> the manual) sounds much simpler.
>
> mmtsb really comes into its own with more sophisticated analyses.
>
> --
> Dr. David Smith
> Division of Organic Chemistry and Biochemistry
> Rudjer Boskovic Institute
> Bijenicka 54
> 10002 Zagreb, Croatia
> tel: +385-1-4561252
> fax: +385-1-4561118
>
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>

Murat CETINKAYA
Biomolecular Materials Lab,
Dept. of Engr. Science and Mechanics,
The Pennsylvania State University,
University Park, PA 16802
office: (814) 863 9967
web: www.personal.psu.edu/muc176
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