AMBER Archive (2004)

Subject: Re: AMBER: Simulated anealling

From: David A. Case (
Date: Thu Jun 03 2004 - 21:34:17 CDT

On Thu, Jun 03, 2004, wrote:
> Hi all,
> I ha dwritten about the protocol regarding the simulated anealling
> earlier. I also want to share a problem which i am facing with this
> protcol. After running for for about 40 ps it showed the following error:
> Frac coord min, max: -1.17673771E-05 0.846951537
> The system has extended beyond
> the extent of the virtual box.

You need to visually look at your simulation and try to figure out what it
happening that makes it move so far from the starting structure. It could
be the high temperature, it could be the model or the contraints, etc. There
is no generic solution. But when the system extends beyond the virtual box,
in almost all cases this means that something very bad is happening. You
need to look for the cause, not just fix the symptom.

...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