diff --git a/min.sh b/min.sh new file mode 100755 index 0000000000000000000000000000000000000000..695afda724b91c8fdd692104daa1049195b18f60 --- /dev/null +++ b/min.sh @@ -0,0 +1,33 @@ +#!/bin/bash + +#SBATCH --partition=debug_latest +#SBATCH --time=00-00:60:00 +#SBATCH --job-name=dna_min_demo +#SBATCH --nodes=1 +#SBATCH --ntasks-per-node=28 +#SBATCH --cpus-per-task=1 +#SBATCH -o %j_%x.o +#SBATCH -e %j_%x.e +#SBATCH --constraint=op +#SBATCH --constraint=avx2 +#SBATCH --constraint=avx512 + +source $GROMAX/load_gmx.sh +source $GROMAX/gmx_funcs.sh + +# dirs +mkdir -p min +cd min + +# run md +gromax grompp -f ../mdp/min.mdp -c ../top/dna_rdy.gro -p ../top/topol.top -o min.tpr +gromax mdrun -v -deffnm min + +# analysis +minimStats mdrun +gromax energy "Potential" -f "min.edr" -o "min_pot.xvg" +xvg2png -f min_pot -o min_pot -xl 'MD step' -yl 'Potential Energy kcal/mol' -ys -xt 5000 + +# # trajectories +gromax trjconv "Non-Water" -s "min.tpr" -f "min.trr" -o "min_traj.pdb" +gromax trjconv "Non-Water" -s "min.tpr" -f "min.trr" -o "min_fin.pdb" -dump 999