#!/bin/bash --login
#SBATCH --job-name=mdrun_cpu
#SBATCH --output=%x.o%j
#SBATCH --error=%x.e%j
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=8
#SBATCH --cpus-per-task=6
#SBATCH --time=0-04:00:00
#SBATCH --mem=16G
#SBATCH --partition=cpu_guest
#SBATCH --qos=cpu_guest
##SBATCH --account=<account>

shopt -q login_shell || exit 1
test -n "$SLURM_NODELIST" || exit 1
test $SLURM_NNODES -eq 1 || exit 1

module load apptainer
module load gromacs/2025.1/cpu

apptainer run \
    --bind "$PWD:/host_pwd" \
    --pwd /host_pwd \
    "$GROMACS_CONTAINER" \
    gmx mdrun \
        -v \
        -ntmpi $SLURM_TASKS_PER_NODE \
        -ntomp $SLURM_CPUS_PER_TASK \
        -nb cpu \
        -pme cpu \
        -npme 1 \
        -update cpu \
        -bonded cpu \
        -nsteps 100000 \
        -resetstep 90000 \
        -noconfout \
        -dlb no \
        -nstlist 300 \
        -pin on