[gmx-users] Restart a run with different files

[Justin Lemkul]

On 12/23/12 3:21 AM, Davit Hakobyan wrote:
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> Dear Gromacs users,
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> I use Gromacs 4.5.1. The problem relates to the restarting procedure of a run. Usually I restart the run with the "-append" option and now I need to move the ".trr" and ".xtc" files to another directory since they got too big for the directory quota where they were located by now. So, previously the restart line looked like the following:
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> mdrun -append -s system.tpr -c system.gro -g system.log -e system.edr -cpi system.cpt -cpo system.cpt -o system.trr -x system.xtc
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> and now after copying (or just moving) the ".trr" and ".xtc" files to a new directory the restart line looks like:
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> dir=new_dir
> mdrun -append -s system.tpr -c system.gro -g system.log -e
>   system.edr -cpi system.cpt -cpo system.cpt -o ${dir}/system.trr -x ${dir}/system.xtc
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> However, in the latter case Gromacs gives the error "output files not present or named differently:..." complaining that the ".trr" and ".xtc" files could not be found in the location pointed by the checkpoint ".cpt" file. This is even when the copy of the original ".trr" and ".xtc" files were left in their original directory.
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> Could anybody point to a solution or a workaround ?
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Use -noappend and concatenate later.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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