<commit_before>#!/bin/tcsh
#  Batch script for mpirun job on cbio cluster.
#
#
# walltime : maximum wall clock time (hh:mm:ss)
#PBS -l walltime=8:00:00
#
# join stdout and stderr
#PBS -j oe
#
# spool output immediately
#PBS -k oe
#
# specify queue
#PBS -q gpu
#
# nodes: number of 8-core nodes
#   ppn: how many cores per node to use (1 through 8)
#       (you are always charged for the entire node)
#PBS -l nodes=1:ppn=4:gpus=4:shared:gtxtitan
#
# export all my environment variables to the job
##PBS -V
#
# job name (default = name of script file)
#PBS -N p-xylene
#
# specify email
#PBS -M <EMAIL>
#
# mail settings
#PBS -m n
#
# filename for standard output (default = <job_name>.o<job_id>)
# at end of job, it is in directory from which qsub was executed
# remove extra ## from the line below if you want to name your own file
#PBS -o /cbio/jclab/projects/musashi/yank.jchodera/examples/p-xylene/torque.out

cd $PBS_O_WORKDIR

date
mpirun -rmk pbs yank --mpi --verbose
date
<commit_msg>Updated run-torque file<commit_after>#!/bin/tcsh
#  Batch script for mpirun job on cbio cluster.
#
#
# walltime : maximum wall clock time (hh:mm:ss)
#PBS -l walltime=8:00:00
#
# join stdout and stderr
#PBS -j oe
#
# spool output immediately
#PBS -k oe
#
# specify queue
#PBS -q gpu
#
# nodes: number of nodes
#   ppn: how many cores per node to use
#PBS -l nodes=1:ppn=4:gpus=4:shared
#
# export all my environment variables to the job
##PBS -V
#
# job name (default = name of script file)
#PBS -N abl-imatinib-implicit
#
# specify email
#PBS -M <EMAIL>
#
# mail settings
#PBS -m n
#

cd $PBS_O_WORKDIR

# Set up and run simulation in serial mode.

if [ ! -e output ]; then
    echo "Making output directory..."
    mkdir output
fi

# Clean up any leftover files
echo "Cleaning up previous simulation..."
yank cleanup --store=output

# Set up calculation.
echo "Setting up binding free energy calculation..."
yank prepare binding amber --setupdir=setup --ligname=MOL --store=output --iterations=1 --restraints=harmonic --gbsa=OBC2 --temperature=300*kelvin --verbose

# Run the simulation with verbose output:
echo "Running simulation..."
mpirun -rmk pbs yank run --store=output --verbose --mpi
date


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