#!/bin/bash -l

#SBATCH --partition=normal
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=8
#SBATCH --gres=gpu:1
#SBATCH --exclude=linux-05,linux-08,linux-02,linux-03,linux-04,linux-07

#if [ "$(gmx --version | grep "GROMACS version")" != GROMACS*2025.2* ] ; then
#    echo "Version loaded is not 2025.2! Exiting!"
#    exit 1
#fi

if [ -n "$SLURM_CPUS_PER_TASK" ]; then
    NT="-nt $SLURM_CPUS_PER_TASK"
elif [ $(nproc) -lt 9 ] ; then
    NT="-nt $(nproc)"
else
    NT="-nt 8"
fi

WORKDIR="$(dirname $(readlink -f "$0"))"
if [ "${WORKDIR%/*}" = "/var/lib/slurm/slurmd" ] ; then
    WORKDIR="$(pwd)"
fi

mkdir -p "$WORKDIR/out"

export GMX_MAXCONSTRWARN=-1;
gmx -nobackup grompp \
    -f $WORKDIR/mdp_parameters.mdp \
    -o $WORKDIR/tpr_run.tpr \
    -c $WORKDIR/gro_start.gro \
    -r $WORKDIR/gro_start.gro \
    -p $WORKDIR/topology.top \
    -po $WORKDIR/out/mdp_mdout.mdp \
    -maxwarn 6

if [ $? != 0 ] ; then
    echo "grompp failed, exiting"
    exit 1
fi

gmx mdrun \
    -s $WORKDIR/tpr_run.tpr \
    -o $WORKDIR/out/trr_traj.trr \
    -c $WORKDIR/out/out.gro \
    -x $WORKDIR/out/xtc_traj.xtc \
    -e $WORKDIR/out/edr_energy.edr \
    -g $WORKDIR/out/log.log \
    -cpo $WORKDIR/out/state.cpt \
    -cpi $WORKDIR/out/state.cpt \
    -cpt 1 -notunepme -v $NT