#!/bin/bash --login
#SBATCH --job-name=amber20cpu
#SBATCH --output=%x.o%j
#SBATCH --error=%x.e%j
#SBATCH --nodes=2
#SBATCH --ntasks-per-node=16
#SBATCH --time=0-01:00:00
#SBATCH --mem=16G
#SBATCH --partition=cpu
#SBATCH --constraint='broadwell|skylake'
#SBATCH --account=<account>

shopt -q login_shell || exit 1

module load gnu8 openmpi4
module load apptainer/1.0

container='/hpc/share/applications/amber/20/amber-20-cpu'

bind="${GROUP:+$GROUP,}${ARCHIVE:+$ARCHIVE,}${SCRATCH:+$SCRATCH,}$(test -d /node && echo /node)"

mpirun \
apptainer exec ${bind:+--bind $bind} "$container.sif" \
sander.MPI -p complex_azd.prmtop -c complex_azd.inpcrd -ref complex_azd.inpcrd -i min1.in -o min1.out -r min1.crd -O