#!/bin/bash
#SBATCH --job-name=yank_gettrajs
#SBATCH --partition=qgpu
#SBATCH --nodes=1
#SBATCH --cpus-per-task=18
#SBATCH --time=24:00:00
#SBATCH --gres=gpu:v100:1
echo "========= Job started  at `date` =========="
cd $SLURM_SUBMIT_DIR

python=<PATH-TO-PYTHON>
base_executable_path=${python::-6}
# Required variables:
# $interacting_output_dir : Path to the interacting output directory.
# $separated_output_dir : Path to the separated output directory.
# $output_directory : Path to the output directory.

experiment_dir1=$interacting_output_dir/experiments
experiment_dir2=$separated_output_dir/experiments

mkdir extendedendstate_trajs

$base_executable_path/yank analyze extract-trajectory --netcdf=$experiment_dir1/complex.nc --state=0 --trajectory=$output_directory/complex_l1.xtc
$base_executable_path/yank analyze extract-trajectory --netcdf=$experiment_dir1/solvent.nc --state=0 --trajectory=$output_directory/solvent_l1.xtc

$base_executable_path/yank analyze extract-trajectory --netcdf=$experiment_dir2/complex.nc --state=0 --trajectory=$output_directory/complex_l0.xtc
$base_executable_path/yank analyze extract-trajectory --netcdf=$experiment_dir2/solvent.nc --state=0 --trajectory=$output_directory/solvent_l0.xtc

echo "========= Job finished at `date` =========="