AMBER Archive (2003)

Subject: Re: Simple question about sander parameter set

From: Peng Tao (ptao_at_chemistry.ohio-state.edu)
Date: Tue May 13 2003 - 10:19:50 CDT

Dr. Case,

The version of AMBER I used is 7. I used it on ohio super computer center.
The reason I used nrun parameter is that I found it in one tutorial example
.in file.
http://www.amber.ucsf.edu/amber/tutorial/polyA-polyT/equil/mdin

A worse thing is that I misread the manual of AMBER7 by using description of
NRUN in GIBBS section.

When I used nrun paramter, the sander program did run on back ground. When
using bq command, I can see the elapse time did increase. But there is no
any output, only .out file appear, and the size is zero. After exceeding the
set running time for the job, the job was killed and still no output.

Thanks again for your help. I wouldn't use this paramter in sander anymore.

Yours Sincerely,
Peng Tao

Chemistry Department
The Ohio State University

----- Original Message -----
From: "David A. Case" <case_at_scripps.edu>
To: "Peng Tao" <ptao_at_chemistry.ohio-state.edu>
Cc: <amber_at_heimdal.compchem.ucsf.edu>
Sent: Tuesday, May 13, 2003 11:00 AM
Subject: Re: Simple question about sander parameter set

> On Tue, May 13, 2003, Peng Tao wrote:
> >
> > I am trying to use AMBER to do a simple protein MD. When I used NRUN
> > parameter, no matter how long I run sander ( about 100 hours on 8 nodes
> > with 2 cpus on each node), I never got any output.
>
> What version of amber are you using? "nrun" is no longer a valid paramter
> in Amber 7. It could be that the simulation is stopping immediately for
> that reason, and that you are not seeing the error file for some reason.
>
> Are you sure the job that gives no output is actually running?
>
> ..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
> ==================================================================
>
>