Re: AMBER: Problems simulating a big system

From: Jordi Camps <>
Date: Tue, 17 Jul 2007 11:57:13 +0200


I'll try the short run. By the way, the system has been minimized and
equilibrated, but this is the first run of production MD. It is only the
"restart" after the setup process.
Right now I suspect that it can have something to do with the
wall_clock_time defined. No message of the queue system about this limit
being exceeded has been issued. And the time given should be enough to
run the full run, but maybe I was wrong in the time estimation and I
defined a very short time limit.

Thank you for your attention,

Jordi Camps Puchades
Supercomputing research, support and development

Barcelona Supercomputing Center | Instituto Nacional de Bioinformática
                                  | GN6-MN UPC-BSC ( |
Tel. : 934 137 602 | Tel. : 934 037 155
Fax : 934 137 721 | Fax : 934 037 157
c/ Jordi Girona, 29 | c/ Josep Samitier, 1-5
Edifici Nexus II, despatx 1B | PCB, Edifici Modular, PBC32
E-08034 Barcelona | E-08028 Barcelona
Catalunya (Spain) | Catalunya (Spain)

David A. Case escribió:
> On Mon, Jul 16, 2007, Jordi Camps wrote:
>> I'm trying to run a MD simulation of a big system, and I'm getting some
>> trouble with Amber 9.
>> When I run the simulacion with sander (MPI version), the program crashes
>> after a few steps wthout giving further information.
> It's weird that it "crashes after a few steps". Try a short run (10 steps)
> and set ntpr=1. Look at the behavior of the energies to see if something
> points to the problem. Have you minimized the initial coordinates? Have you
> run this system before (i.e, is this a restart of the previously successful
> MD run, or is this the first one?)
> ....dac
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to
> To unsubscribe, send "unsubscribe amber" to
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Wed Jul 18 2007 - 06:07:41 PDT
Custom Search