AMBER Archive (2005)

Subject: Re: AMBER: troubleshooting replica exchange

From: Sergio E. Wong (swon9_at_itsa.ucsf.edu)
Date: Wed Oct 12 2005 - 19:48:45 CDT

> I tried to run md3 several times and it all crashed at the same place
> where all the crd files are about 2/3 size of what it should be and
> one of the crd file is slightly smaller than the other 31 crd files (I
> have 32 replica and it writes out 32 crd files)

It looks like one of the replicas crashed and hence the "slightly shorter"
trajectory. You could 1) visualize the shorter trajectory - Something
wrong will likely be apparent, 2) take the most recent 026.rst file and
start a single temperature simulation to monitor it's behavior. You
should be able to query the the total energy and it's components very
often (more often than you probably did in your replica exchange
simulation).

Good luck

-Sergio
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