AMBER Archive (2004)

Subject: Re: AMBER: NMODE

From: David A. Case (
Date: Fri Apr 09 2004 - 17:46:35 CDT

On Fri, Apr 09, 2004, xiaowei li wrote:

> Hi, I am using NMODE to calculate the frequencies of DNA with 12 Base
> Pairs in vacuo. My computer has two 1.53 GHz AMD Athlon K7 MP processors
> with 256KB of cache (per cpu) and 1 GB of RAM. First, I tried to
> minimize the energy by set nrun=4. However, after one week (168 hrs),
> the job is still not finished. I want to know generally how long it
> will take to finish evergy minization by nmode for 12 base pairs DNA in
> vacuo . And how long does it take to get the frequencies after energy
> minization. Thank you in advance

It is generally recommended to first minimize in sander, then use ntrun=1
in mode. However, the ntrun=4 option _should_ print out results every step,
so you should be able to tell from the output how well (or poorly) the
minimization is going. You only need to get to an RMS gradient of around
10**-4. 168 hours is way too long for a 12-base pair DNA: that should be
done in a few hours at most.

...good luck...dac


================================================================== David A. Case | e-mail: 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 | ================================================================== ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to To unsubscribe, send "unsubscribe amber" to