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Talk:Mod:Hunt Research Group/ChemShell cx1

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Here's an example submit script to run the QM/MM single point energy example calculation.

#/bin/sh
#PBS -l walltime=48:00:00
#PBS -l mem=2600MB
#PBS -j oe

module load dl_poly/2.19 intel-suite mpi
module load gaussian/g09
module load chemshell/3.5.0

cp $PBS_O_WORKDIR/energy.chm $TMPDIR
cp $PBS_O_WORKDIR/ff.dat $TMPDIR
cp $PBS_O_WORKDIR/cu_18water.pun $TMPDIR

cd $TMPDIR
mpiexec chemsh.x energy.chm > energy.out

cp $TMPDIR/* $PBS_O_WORKDIR/

The following submit script will request multiple processors to run the QM/MM MD example simulation.

#/bin/sh
#PBS -l walltime=48:00:00
#PBS -l select=1:ncpus=8:mem=2600MB
#PBS -j oe

module load dl_poly/2.19 intel-suite mpi
module load gaussian/g09
module load chemshell/3.5.0

cp $PBS_O_WORKDIR/energy.chm $TMPDIR
cp $PBS_O_WORKDIR/ff.dat $TMPDIR
cp $PBS_O_WORKDIR/cu_18water_qmmm_opt.pun $TMPDIR

cd $TMPDIR
mpiexec chemsh.x md.chm > md.out

cp $TMPDIR/* $PBS_O_WORKDIR/

If multiple processors are to be used, remember to specify that in the .chm input. For example, you can request multiple processors for the Gaussian part a job using the nproc keyword as shown below:

theory= hybrid : { coupling=shift  \
                   qm_region = {1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22} \
                   qm_theory=gaussian : { nproc=8 basis=6-311g g98_mem=80000000 charge=2 mult=2 hamiltonian=b3lyp } \
                   mm_theory=dl_poly : mm_defs=ff.dat } \
                   timestep = 0.001  ensemble = NVE
                 }