This section inclused:

• A sample of Packmole input file.
• Few Samples of CPPTRAJ input files.
• A sample of tleap input file.
• A python code to generate multiple PBS files for different job sumissions.
• A python code to generate multiple CPPTRAJ input files for calculations.

• Class of mdAnalysis which helps with different types of analysis in MD simulations.

• Class of mdAnalysis which can perform different steps of adaptive sampling with or without making MSM in each round.

• More samples of using CPPTRAJ.

• Sample codes for tcl programming in VMD.