17-Jan-2023 12:01:54: Creating md2path directory in C:\Users\mahdi\Desktop\PhD EPFL\Manuscripts\Flex pep ago des 2022\Revisions\AlloDy_rev\Demo
17-Jan-2023 12:02:35: Transformed .xtc files to .dcd files with the following command: "vmd -dispdev text -e C:\Users\mahdi\Documents\md2path\load_save.tcl -args C:\Users\mahdi\Desktop\PhD EPFL\Manuscripts\Flex pep ago des 2022\Revisions\AlloDy_rev\Demo 3 20 C:\Users\mahdi\Desktop\PhD EPFL\Manuscripts\Flex pep ago des 2022\Revisions\AlloDy_rev\Demo\prot.pdb step7_noPBC_prot.xtc"
17-Jan-2023 12:05:04: Transformed .xtc files to .dcd files with the following command: "vmd -dispdev text -e C:\Users\mahdi\Documents\md2path\load_save.tcl -args C:\Users\mahdi\Desktop 3 20 C:\Users\mahdi\Desktop\PhD EPFL\Manuscripts\Flex pep ago des 2022\Revisions\AlloDy_rev\Demo\prot.pdb step7_noPBC_prot.xtc"
17-Jan-2023 12:10:16: RMSD plotted and saved successfully
17-Jan-2023 12:10:17: Receptor RMSF plotted and saved successfully
17-Jan-2023 12:10:18: Do not forget ligand RMSF! It has also been plotted and saved

17-Jan-2023 12:10:24: Calculating contact map of receptor with ligand
17-Jan-2023 12:10:39: PCA analysis commenced
17-Jan-2023 12:10:39: Creating pca directory in C:\Users\mahdi\Desktop\PhD EPFL\Manuscripts\Flex pep ago des 2022\Revisions\AlloDy_rev\Demo\md2path
17-Jan-2023 12:10:40: PCA clustering of ligand pose performed!
17-Jan-2023 12:11:01: frame_centers saved to pcaCenterFrame_runxt
pdbs saved to ligandpca.pdb and ligandReceptorpca.pdb
17-Jan-2023 12:14:46: S2 convergence calculated and plotted
