#!/bin/bash --login
#$ -N jobname_namd

# job resources in Mebibytes
#$ -l mem_free=500M

# wall clock time in HH:MM:SS
#$ -l h_rt=00:10:00

# choose any host in cluster18
#$ -l cluster18

# use five CPU cores at all
#$ -pe mp 5

# ask for one GPU adapter card
#$ -l gpus=1

#$ -cwd

# mail sending options
#$ -o stdout.out
#$ -e stderr.out
#$ -j no
#$ -m b,e  
#$ -M [name_of_your_mailbox]


module load cuda/8.0 namd/2.12-cuda
namd2 +p 5 inputfile > outputfile