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Job submission to run Amber PMEMD.cuda on  GPU node on Spruce:

#!/bin/bash

#PBS -q jbmertz_gpu
#PBS -m ae
#PBS -M [YOUR EMAIL HERE]  #change
#PBS -N [YOUR JOB NAME HERE]  #change
#PBS -l walltime=3999:00:00     #change
#PBS -l gpus=1

module load chemistry/amber14
GPUSLOT=$(cat $PBS_GPUFILE | tail -c 2)
export CUDA_VISIBLE_DEVICES="$GPUSLOT"


scratch=/scratch/jufeng/bpr-run1  #change
cd $scratch


pmemd.cuda ....# your job command
Job submission to run Gromacs on Spruce:

#!/bin/bash

#PBS -q jbmertz
#PBS -m ae
#PBS -M  [xx]  # ur email address here
#PBS -N  [xx] # put ur job name here
#PBS -l walltime=99:00:00  #change according to how long ur job is
#PBS -l nodes=1:ppn=16   #change according to how many cores u want to request

module load chemistry/gromacs/5.0.5
cd xx  #go to directory where u want to run ur job
mdrun_mpi -s top13.tpr  # change according to ur gromacs command

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