[gmx-users] Umbrella from checkpoint file

Steven Neumann s.neumann08 at gmail.com
Mon Apr 16 12:13:38 CEST 2012

Dear Gmx Users,

I am doing Umbrella Sampling on the cluster with wall time of 72h and
Temporary Directory ($TMP) where all jobs and temporary files are stored
and removed. I want to run my umbrella sampling window from previous
checkpoint file:

module load gromacs/4.5.4

module load mpi

module load intel-suite/11.1

 cp /work//Umbrella/8/umbrella0* $TMP

cp /work/Umbrella/8/pullf-umbrella0.xvg $TMP

cp /work/Umbrella/8/pullx-umbrella0.xvg $TMP

cp -r /Umbrella/8/charmm27mod.ff/ $TMP

pbsexec mpiexec mdrun -s umbrella0.tpr -cpi umbrella0.cpt -deffnm umbrella0
-pf pullf-umbrella0.xvg -px pullx-umbrella0.xvg

cp $TMP/umbrella0* /work//Umbrella/8

cp $TMP/pullf-umbrella0.xvg /work/Umbrella/8

cp $TMP/pullx-umbrella0.xvg /work//Umbrella/8

So every time I need to copy all my files then run a job and copy them
back. My question: If my files are deleted from temporary directory does it
mean that final pullf.xvg and pullx.xvg files will not be updtated from
previous simulation but created new? Is there any solution to avoid this??

Thank you,

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