AMBER Archive (2008)

Subject: Re: AMBER: Problems in execution of Replica Exchange calculations Amber 9.0

From: David A. Case (case_at_scripps.edu)
Date: Thu Jan 24 2008 - 11:25:09 CST

On Thu, Jan 24, 2008, rebeca_at_mmb.pcb.ub.es wrote:

> I am trying to do Replica Exchange Molecular dynamics using Amber 9.0 and I am
> having problems in the execution.

There are quite a few examples in the amber9/test/rem_* directories. Make
sure that "make test.sander.REM" gives good results for your system, and study
those examples to see how (if at all) they differ from your inputs. That
might provide a clue.

Also, just run short versions of these jobs on a desktop machine (i.e. without
the queuing system.) It sometimes happens that outputs or errors get lost
that you could see if you ran it manually.

...good luck...dac

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