Re: AMBER: replica exchange hangs

From: Peter Varnai <>
Date: Wed, 1 Mar 2006 18:56:21 +0000 (GMT)

Dear Carlos,

> One thing to check in your restart files that you use as input
> is to ensure that all have different T in the restart file (2nd line, third
> number, only in REMD restarts). It can be possible if a job
> crashes that the restarts are not all at the same time point and
> matching temperatures will cause a crash. This part is fixed in Amber
> 9 along with some other changes.

That is probably the problem ... now that I am checking for this I see
that the job was killed by the queue system and indeed the two rst
files had the same temperature! However, when I restarted the job I
had >1000 "successful" exchanges. Probably I should throw that
part away now ... but it can still happen unnoticed that after a crash
not all replicas have the correct temperatures in the ensembles. Will
this latter cause problems or it will reequilibrate quickly?

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Sun Mar 05 2006 - 06:10:12 PST
Custom Search