Re: Incomplete coord file after crash

From: Michael Cooney <>
Date: Thu 25 Jan 2001 16:24:46 -0500 (EST)

Dear Dr. Ross,
Thanks very much for the advice--I tried it and it seems to have worked.
Just one other question--should I do the same thing to the restart file
before restarting the calculation? I ask this because I noticed the times
in the restarted run have 0.1 ps added to them, i.e. 400.1 ps instead of
400.0 ps. I assume this repair process will also work for a restart file.

Michael Cooney

On Thu, 25 Jan 2001, Bill Ross wrote:

> the CRD file from the job that
> crashed is incomplete. As a result I cannot carry out certain CARNAL
> procedures, namely stripping waters from the files after merging the
> incomplete file with the new file from the restarted job.
> The output gives the following message:
> bmd_merged.crd: too many numbers on box line for mdcrd format -
> bad coord file or carnal bug
> Before merging the files, try reading the damaged file in carnal &
> writing it out unmodified - the last, damaged crdset will be ignored
> and the new file should be ok for further operations.
> Bill Ross
Received on Thu Jan 25 2001 - 13:24:46 PST
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