Submitting a Amber Job to SGE

#!/bin/csh
# Example for 12 processors.
#$ -N amber_job_name
#$ -pe mpi-12 12
#$ -M afs_id@nd.edu
#$ -m ae
# Do not set automatic restart as Amber does not recover well

# Increase the MPI buffer
setenv P4_GLOBMEMSIZE 268435456

module load amber/16.0

mpirun -np $NSLOTS $AMBERHOME/bin/sander.MPI  -O -i file.in -o file.out -c prev_file.restrt -p file.prmtop -r file.restrt -x file.cmd -ref prev_file.restrt

Replace file.{in,out,restrt,prmtop,cmd} name with your files.

The serial version of the previous script is:

#!/bin/csh
#$ -N amber_job_name
#$ -M afs_id@nd.edu
#$ -m ae
# Do not set automatic restart as Amber does not recover well

# Increase the MPI buffer
setenv P4_GLOBMEMSIZE 268435456

module load amber/16.0

$AMBERHOME/bin/sander -O -i file.in -o file.out -c prev_file.restrt -p file.prmtop -r file.restrt -x file.cmd -ref prev_file.restrt


For further information, please consult the Amber documentation: http://ambermd.org/doc12/Amber17.pdf