Re: AMBER: nonbonded interactions

From: Svetlana Kirillova <>
Date: Wed, 23 Mar 2005 10:23:47 +0100 (CET)

Dear M. Case,

Thank you very much for your reply.

Best regards,
Svetlana Kirillova

>Date: Tue, 22 Mar 2005 21:38:08 -0800
>From: "David A. Case" <>
>Subject: Re: AMBER: nonbonded interaction
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>On Tue, Mar 22, 2005, Svetlana Kirillova wrote:
>> We need of all methods for
>> minimization of energy: conjugate gradient and steepest descent of SANDER
>> 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 - 09:53:01 PST
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