#!/bin/bash -l
#SBATCH --partition=compute             # specific partition to gpu node
#SBATCH -N 4 --ntasks-per-node=40       # for requset 4 compute node with 40 cpu-cores
#SBATCH --time=120:00:00                # job time limit <hr:min:sec>
#SBATCH --account=projXXXX              # change projXXXX  to your project account
#SBATCH --job-name=testMD

module purge                            # purge all module
module load bzip2/1.0.8-GCCcore-8.3.0
module load XZ/5.2.4-GCCcore-8.3.0
module load GCC/8.3.0
module load OpenMPI/3.1.4-gcccuda-2019b

WORKDIR=$SLURM_SUBMIT_DIR
######################################################
# nothing should need changed below here to run unless you do not
export AMBER_PREFIX="/tarafs/data/project/proj0XXXX/amber20_src"
export AMBERHOME=/tarafs/data/project/proj0XXXX/amber20_src
export PATH="${AMBER_PREFIX}/bin:${PATH}"
# Add location of Amber Python modules to default Python search path
cd $AMBERHOME
source amber.sh
######################################################
cd $WORKDIR

srun pmemd.MPI -O -i input.in -o md.out -p system.top -c md_2.restrt -ref md_2.restrt -r md_1.restrt -x md_1.nc -v mdvel

export AMBER_PREFIX="/tarafs/data/project/proj0999/amber20_src"
export AMBERHOME=/tarafs/data/project/proj0999/amber20_src

#!/bin/bash -l
#SBATCH --partition=gpu                 # specific partition to gpu node
#SBATCH --nodes=1                       # for requset 1 compute node with 40 cpu-cores
#SBATCH --time=120:00:00                # job time limit <hr:min:sec>
#SBATCH --account=projXXXX              # change projXXXX  to your project account
#SBATCH --job-name=testMD

module purge                            # purge all module
module load bzip2/1.0.8-GCCcore-8.3.0
module load XZ/5.2.4-GCCcore-8.3.0
module load CUDA/10.1.243-GCC-8.3.0
module load gcccuda/2019b
module load OpenMPI/3.1.4-gcccuda-2019b

WORKDIR=$SLURM_SUBMIT_DIR
######################################################
# nothing should need changed below here to run unless you do not
export AMBER_PREFIX="/tarafs/data/project/proj0XXXX/amber20_src"
export AMBERHOME=/tarafs/data/project/proj0XXXX/amber20_src
export PATH="${AMBER_PREFIX}/bin:${PATH}"
# Add location of Amber Python modules to default Python search path
cd $AMBERHOME
source amber.sh
######################################################
cd $WORKDIR

srun -n 2 pmemd.cuda.MPI -O -i input.in -o md.out -p system.top -c md_2.restrt -ref md_2.restrt -r md_1.restrt -x md_1.nc -v mdvel

#!/bin/bash -l
#SBATCH --partition=devel               # specific partition to compute node
#SBATCH --nodes=1 --ntasks-per-node=1   # for requset 1 compute node with 1 cpu-core
#SBATCH --account=projXXXX              # change projXXXX  to your project account
#SBATCH --time=2:00:00                  # job time limit <hr:min:sec>
#SBATCH --account=projXXXX              # change projXXXX  to your project account
#SBATCH --job-name=mmpbsa

module purge                            # purge all module
module load bzip2/1.0.8-GCCcore-8.3.0
module load XZ/5.2.4-GCCcore-8.3.0
module load GCC/8.3.0
module load OpenMPI/3.1.4-GCC-8.3.0

WORKDIR=$SLURM_SUBMIT_DIR
######################################################
# nothing should need changed below here to run unless you do not
export AMBER_PREFIX="/tarafs/data/project/proj0XXXX/amber20_src"
export AMBERHOME=/tarafs/data/project/proj0XXXX/amber20_src
export PATH="${AMBER_PREFIX}/bin:${PATH}"
# Add location of Amber Python modules to default Python search path
cd $AMBERHOME
source amber.sh

######################################################
cd $WORKDIR

cpptraj -i  rmsd.in   >  rmsd.out