AMBER Archive (2006)

Subject: Re: AMBER: replica exchange hangs

From: Peter Varnai (pv232_at_cam.ac.uk)
Date: Wed Mar 01 2006 - 12:56:21 CST

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?

Thanks,
Peter
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