Re: AMBER: Time to minimize the energy by NMODE

From: David A. Case <>
Date: Wed, 14 Apr 2004 15:54:10 -0700

On Wed, Apr 14, 2004, xiaowei li wrote:

> Hi, I want to calculate the normal frequencies of DNA with 5 base pairs.
> So I take following steps to get it.
> First, using SANDER to minimize the energy, and I got RMS=4.467E-01, and
> sandermin.rst.
> Second, using NMODE(ntrun=4) to minimize sandermin.rst to get RMS is in
> the order of 10^-4.
> As David has emailed me before, it just takes a few hours to finish
> NMODE minimization ( My computer has two 1.53 GHz AMD Athlon K7 MP
> processors with 256KB of cache (per cpu) and 1 GB of RAM).
> However, NMODE minimization has run about 50 hrs on my computer and it
> is not finished yet. Is there anything wrong with my case?

There is certainly something wrong. I ran a Newton-Raphson minimization
on a 10-base pair RNA (640 atoms, should be about twice as big as your
system), and each step took about 10 seconds on a 2.4 GHz Pentium. You
should certainly begin seeing output within a few seconds of starting
your job.

Of course, do the obvious things like running 10 steps, rather than 500,
using the "top" command to make sure the job is really running, etc.
(I am assuming [forgot if you said this before] that nmode passes the tests
on your computer.) What happens if you set ntrun=1 instead of 4?

You should bear in mind that the minimum in a gb force field and that in
a vacuum force field will be quite different. You will probably want to
use something like epsilon=4r if you need to get normal modes of a nucleic

....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            |
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Received on Thu Apr 15 2004 - 00:53:00 PDT
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