• a. Read the trajectory file ('.dcd' as file extension), with python script 'readDCDFile.py',you will get the file name 'distance.txt', which includes all the oxygen atom information and coordinates.
• b. Cluster all the water oxygen coordinated in the 'distance.txt' file to obtain the centers.
• c. Optimizing the centers obtained in the last step to combine centers near each other.
• d. Read the center coordinates and save H2O coordinates according to each center. 'getH2OCoordidateAll.py' is used in this step, and the coordinates for H and O atoms were saved into 'WW_allCentre_H2O.txt'.
• a. Using 'SW_TranEntr.py' to calculate the protein-water correlation entropy for each water molecule. The output file is saves in 'SW.dat'.
• a. 'WW_trans.py' is used to calculate the translational entropy of each water molecules. The output file is saved in 'WW_Trans.dat'.
• b.'WW_orientation_R3.py' or 'WW_orientation_R5.py' can be used to save the entropy wo water-water orientational entropy of each water-water correlation. The output file is saved in 'water_Orien.txt'.
• a. NAMDenergy in VMD is used to calculate the interaction energy of each system. 'energy_tcl_generation.py' is used to get the tcl file for namd energy calculation. PLS remind that include the namd directory and add -exe in each calculation.
• b. Each interaction energy is extracted with 'extract_energy.py'.