#!/bin/bash

python ~/Documents/md_scripts/plot_md.py rmsd 1xck_rmsd '1XCK -MgATP-' 'Time (ns)' 'RMSd (Å)' '0' '0' 'rmsd.dat'

python ~/Documents/md_scripts/plot_md.py rmsd 1xck_cis_trans '1XCK -MgATP- cis and trans rings' 'Time (ns)' 'RMSd (Å)' '0' '5' rmsd_cis_ring.dat rmsd_trans_ring.dat 'Cis ring' 'Trans ring' '0' '5'

python ~/Documents/md_scripts/plot_md.py rmsd 1xck_cis_chains '1XCK -MgATP- cis ring chains' 'Time (ns)' 'RMSd (Å)' '0' '5' rmsd_chainA.dat rmsd_chainB.dat rmsd_chainC.dat rmsd_chainD.dat rmsd_chainE.dat rmsd_chainF.dat rmsd_chainG.dat A B C D E F G '0' '5'

python ~/Documents/md_scripts/plot_md.py rmsd 1xck_trans_chains '1XCK -MgATP- trans ring chains' 'Time (ns)' 'RMSd (Å)' 0 5 rmsd_chainH.dat rmsd_chainI.dat rmsd_chainJ.dat rmsd_chainK.dat rmsd_chainL.dat rmsd_chainM.dat rmsd_chainN.dat H I J K L M N 0 5

python ~/Documents/md_scripts/plot_md.py rmsd 1xck_A_domains '1XCK -MgATP- chain A domains' 'Time (ns)' 'RMSd (Å)' 0 5 rmsd_equatorial.dat rmsd_apical.dat rmsd_intermediate.dat Equatorial Apical Intermediate 0 5 

python ~/Documents/md_scripts/plot_md.py distance 1xck_inter_ring_distance '1XCK -MgATP- inter ring distance' 'Time (ns)' 'Inter ring distance (Å)' 0 0 inter_ring_distance.dat