OpenMM-Amber_Charmm

Created by [email protected], based on the official openmm documentation in https://openmm.org/documentation #This notebook can be divided to three parts.

1. Openmm installation and a test simulation
2. Openmm simulation with Amber input, i.e., a prmtop file, and a (inp)crd file
3. Openmm simulation with VMD/Charmm input, i.e., a psf file and a pdb file.

Note: The methods of how to generate Amber or VMD/Charmm input are not included here, you are supposed to be confident with at least one of them before using this notebook. A good example of Amber input generation could be a newly published paper https://github.com/pablo-arantes/Making-it-rain; An example of VMD/Charmm procedure could be one of my repository in https://github.com/quantaosun/NAMD-MD

Note, the 3htb, example, i.e., the first OpenMM simulation is just for testing purpose, to verify our simulation software (openmm) is working. For a more proper simulation you should use the following two, i.e., the Amber input version or the VMD/Charmm input verion.