#!/bin/bash

# Comparing RMSd of chain A -APO- of three simulations
python ~/Documents/md_scripts/plot_md.py rmsd 1xck_chainA_apo_extracted '1XCK -APO- chainA' 'Time (ns)' 'RMSd (Å)' '50' '8' ../1XCK_chainA/121_1XCK_chainA_apo/traj/rmsd.dat 117_1XCK_hepta/traj/rmsd.dat 116_1XCK_apo/traj/rmsd.dat 'Chain A from single subunit simulation' 'Chain A from heptamer simulation' 'Chain A from double ring simulation' '0' '8'

# Comparing RMSd of chain A -MgATP- of three simulations
python ~/Documents/md_scripts/plot_md.py rmsd 1xck_chainA_MgATP_extracted '1XCK -MgATP- chain A' 'Time (ns)' 'RMSd (Å)' '50' '8' ../1XCK_chainA/126_1XCK_chainA_MGATP/traj/rmsd.dat 128_1XCK_hepta_MGATP/traj/rmsd.dat 129_1XCK_MGATP/traj/rmsd.dat 'Chain A from single subunit simulation' 'Chain A from heptamer simulation' 'Chain A from double ring simulation' '0' '8'

# Comparing RMSd of simulation of the complex, w/wo MgATP 
python ~/Documents/md_scripts/plot_md.py rmsd 1xck_wwo_mgatp '1XCK -double ring- bound vs unbound' 'Time (ns)' 'RMSd (Å)' 50 6 116_1XCK_apo/traj/rmsd.dat 129_1XCK_MGATP/traj/rmsd.dat 'Without MgATP' 'With MgATP' 0 6 

# Comparing RMSd of simulation of the complex, CIS-ring only w/wo MgATP
python ~/Documents/md_scripts/plot_md.py rmsd 1xck_cis_wwo_mgatp '1XCK -cis ring- bound vs unbound' 'Time (ns)' 'RMSd (Å)' 50 6 116_1XCK_apo/traj/rmsd_cis_ring.dat 129_1XCK_MGATP/traj/rmsd_cis_ring.dat 'Without MgATP' 'With MgATP' 0 6
 
# Comparing RMSd of simulation of the complex, TRANS-ring only w/wo MgATP
python ~/Documents/md_scripts/plot_md.py rmsd 1xck_trans_wwo_mgatp '1XCK -trans ring- bound vs unbound' 'Time (ns)' 'RMSd (Å)' 50 6 116_1XCK_apo/traj/rmsd_trans_ring.dat 129_1XCK_MGATP/traj/rmsd_trans_ring.dat 'Without MgATP' 'With MgATP' 0 6

# Comparing RMSd of simulation of the complex, CHAIN A only w/wo MgATP
python ~/Documents/md_scripts/plot_md.py rmsd 1xck_chainA_wwo_mgatp '1XCK -chain A- bound vs unbound' 'Time (ns)' 'RMSd (Å)' 50 6 116_1XCK_apo/traj/rmsd_chainA.dat 129_1XCK_MGATP/traj/rmsd_chainA.dat 'Without MgATP' 'With MgATP' 0 6

# Comparing RMSd of simulation of the complex, EQUATORIAL A only w/wo MgATP
python ~/Documents/md_scripts/plot_md.py rmsd 1xck_A_equatorial_wwo_mgatp '1XCK -equatorial- bound vs unbound' 'Time (ns)' 'RMSd (Å)' 50 6 116_1XCK_apo/traj/rmsd_equatorial.dat 129_1XCK_MGATP/traj/rmsd_equatorial.dat 'Without MgATP' 'With MgATP' 0 6

# Comparing RMSd of simulation of the complex, INTERMEDIATE A only w/wo MgATP
python ~/Documents/md_scripts/plot_md.py rmsd 1xck_A_intermediate_wwo_mgatp '1XCK -intermediate- bound vs unbound' 'Time (ns)' 'RMSd (Å)' 50 6 116_1XCK_apo/traj/rmsd_intermediate.dat 129_1XCK_MGATP/traj/rmsd_intermediate.dat 'Without MgATP' 'With MgATP' 0 6

# Comparing RMSd of simulation of the complex, APICAL A only w/wo MgATP
python ~/Documents/md_scripts/plot_md.py rmsd 1xck_A_apical_wwo_mgatp '1XCK -apical- bound vs unbound' 'Time (ns)' 'RMSd (Å)' 50 6 116_1XCK_apo/traj/rmsd_apical.dat 129_1XCK_MGATP/traj/rmsd_apical.dat 'Without MgATP' 'With MgATP' 0 6


# Comparing RMSd of simulations of heptamer, w/wo MgATP
python ~/Documents/md_scripts/plot_md.py rmsd 1xck_hept_wwo_mgatp '1XCK -heptamer- bound vs unbound' 'Time (ns)' 'RMSd (Å)' 50 6 117_1XCK_hepta/traj/rmsd.dat 128_1XCK_hepta_MGATP/traj/rmsd.dat 'Without MgATP' 'With MgATP' 0 6

# Comparing inter ring distance, w/wo MgATP
python ~/Documents/md_scripts/plot_md.py rmsd 1xck_interring_distance_wwo_mgatp '1XCK inter-ring distance, bound vs unbound' 'Time (ns)' 'Inter ring distance (Å)' 50 0 116_1XCK_apo/traj/inter_ring_distance.dat 129_1XCK_MGATP/traj/inter_ring_distance.dat 'Without MgATP' 'With MgATP' 3 33