conda activate md
# Toy example: run 10 ps NVT and NPT equilibration and 10 ps product simulation
# For real simulation use at least 1ns --md_time 1 --nvt_time 1000 --npt_time 1000
run_md -p protein_HIS.pdb -l ligand.mol --md_time 0.01 --nvt_time 10 --npt_time 10 --ncpu 8 -d mdrun
run_gbsa -i mdrun/md_files/md_run/protein_HIS_1ke7_LS3_replica1/
run_prolif -i mdrun/md_files/md_run/protein_HIS_1ke7_LS3_replica1/ -s 1
prolif_drawmap -i prolif_output_*start-time*.csv --width 6 --height 8 --base_size 12 --occupancy 0.6
