AMBER Archive (2004)

Subject: Re: AMBER: questions about NMODE

From: xhu1_at_memphis.edu
Date: Thu Apr 29 2004 - 18:34:08 CDT

Dear Dr. Dac,

You are right. I used the default values for nmode, which is different
from the default values in sander. After correcting these values,
nmode works! Thank you so much!

Regards

Xiaohua

> Are you using the same dielectric model in the two calculations? If
> everything else is the same except for the electrostatics, then it
> shouldbe possible for you to track down the origin of the
differences.
>
> ...dac
>
> --
>
> ==================================================================
> David A. Case | e-mail: case_at_scripps.edu
> Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
> The Scripps Research Institute | phone: +1-858-784-9768
> 10550 N. Torrey Pines Rd. | home page:
> La Jolla CA 92037 USA | http://www.scripps.edu/case
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