AMBER is a highly parallized suite of biomolecular simulation programs which use MPI and OpenMP on CPUs or CUDA (in combination with MPI) to run on GPUs.
Amber is distributed in two parts: AmberTools and Amber. Amber is a package of molecular simulation programs, AmberTools contains a collection of useful software to analyze and modify MD data. You can find a comprehensive manual here.
The following example runs MMPBSA.py.MPI on 20 identical CPUs. Each of the called Sander jobs (used for surface and energy calculation) may take up to 4G of RAM - for bigger systems this has to be adjusted. The code below runs a 'stability calculation' for a single system. For a comprehensive overview the the AMBER18 manual.
Keep in mind, that MMPBSA calculations are more demanding in terms of memory than MMGBSA jobs.
#!/bin/bash
#PBS -l walltime=XX:YY:ZZ
#PBS -l select=20:ncpus=1:mpiprocs=1:mem=4G
#PBS -l place=group=arch
#PBS -r n
#PBS -N Job Name
#PBS -A Project Name
# input files
INFILE=MMPBSA.infile
EOFILE=Output.dat
PRMTOP=Topology.prmtop
TRAJ=Trajectory.nc
# load Amber
module load Amber/18
# go to work dir
cd $PBS_O_WORKDIR
# def executable
MPI_EXE=`which MMPBSA.py.MPI`
# generate log file
LOGFILE=$PBS_O_WORKDIR/$PBS_JOBNAME"."$PBS_JOBID".log"
echo "$PBS_JOBID ($PBS_JOBNAME) @ `hostname` at `date` in "$PBS_O_WORKDIR" START" > $LOGFILE
echo "`date +"%d.%m.%Y-%T"`" >> $LOGFILE
echo >> $LOGFILE
echo "GLOBAL PARAMETERS">> $LOGFILE
echo "---------------------------" >> $LOGFILE
echo "Node : "$HOSTNAME >> $LOGFILE
echo "Arch : "$ARCH >> $LOGFILE
echo "---------------------------" >> $LOGFILE
echo "RunDir : "$PBS_O_WORKDIR >> $LOGFILE
#
MPICPUS=$(cat $PBS_NODEFILE | wc -l)
echo "# MPI CPUs: ${MPICPUS}" >> $LOGFILE
mpirun $MPI_EXE -i $INFILE -eo $EOFILE -cp $PRMTOP -y $TRAJ >>$LOGFILE
qstat -f $PBS_JOBID >> $LOGFILE
echo "$PBS_JOBID ($PBS_JOBNAME) @ `hostname` at `date` in "$RUNDIR" END" >> $LOGFILE
echo "`date +"%d.%m.%Y-%T"`" >> $LOGFILE |