Re: AMBER: nonbonded interaction

From: David A. Case <>
Date: Tue, 22 Mar 2005 21:38:08 -0800

On Tue, Mar 22, 2005, Svetlana Kirillova wrote:
> We need of all methods for
> minimization of energy: conjugate gradient and steepest descent of SANDER module
> and also Newton-Raphson of NMODE module. But I can't receive the same results
> for nonbonded interactions (attachments files):
> VDWAALS = -238.3023 EEL = -1675.1841 in SANDER
> E-NONB = -0.24552E+03 E-ELE = -0.16964E+04 in NMODE.

Sander uses an atom=based cutoff, and nmode uses a residue based cutoff.
If you are going to all the trouble to do Newton-Raphson minimization,
you should set the cutoff to a very large value (e.g. 9999) so that all
interactions will be included. Then you should be able to get the same
results from both programs. An "infinite" cutoff is also needed to get
very accurate minima.

....hope this helps....dac

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Received on Wed Mar 23 2005 - 05:53:01 PST
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