This is how my log file look like:
Starting script at:Mon Jun 11 10:15:44 MYT 2012
>
> Job 3 started at:Mon Jun 11 10:15:44 MYT 2012
> md3.mdcrd: 60.8% -- replaced with md3.mdcrd.gz
> Job 3 finished at:Wed Jun 13 00:34:51 MYT 2012
> .CURRENT: Command not found.
> Job 3 started at:Wed Jun 13 00:34:51 MYT 2012
> gzip: md3.mdcrd.gz already exists; do you wish to overwrite (y or n)?
>
At the end of MD, i only get one file when 5 files of 200ps is expected.
Can you help? Thanks
On Tue, Jun 19, 2012 at 11:58 AM, Niel Henriksen <niel.henriksen.utah.edu>wrote:
>
> There are many possibilities. If you could post any
> error messages from the output files that would
> help us determine the problem.
>
> --Niel
> ________________________________________
> From: Tommy Yap [tommyyap87.gmail.com]
> Sent: Monday, June 18, 2012 9:06 PM
> To: AMBER Mailing List
> Subject: [AMBER] Script error to restart MD automatically
>
> Dear all,
>
> I used this script to restart my MD runs automatically and it worked well
> in AMBER8. But now I am using AMBER11 and the script does not seem to work
> anymore. Can anyone help to check if there is any problem with the script?
>
> My script looks like this:
>
> #!/bin/csh
> > set AMBERHOME="/usr/local/amber11"
> > set START=3
> > set END=7
> > set CURRENT=$START
> > set INPUT=0
> >
> > echo -n "Starting script at:"
> > date
> > echo ""
> >
> > while ($CURRENT <= $END)
> > echo -n "Job $CURRENT started at:"
> > date
> > . INPUT = $CURRENT - 1
> > $AMBERHOME/exe/sander -O -i md_short.in -o md$CURRENT.out -p
> > alasub_wat.prmtop -c md$INPUT.rst -r md$CURRENT.rst -x md$CURRENT.mdcrd
> > gzip -9 -v md$CURRENT.mdcrd
> > echo -n "Job $CURRENT finished at:"
> > date
> > .CURRENT = CURRENT + 1
> > end
> > echo "YES!! JOB DONE!!"
> >
>
> Please help. Thanks
>
> -TOMMY-
> --
> Regards,
> Tommy Yap
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Regards,
Tommy Yap
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Received on Mon Jun 18 2012 - 22:00:02 PDT
