GridMAT-MD membrane analysis program

Python interface for Enhanced Monte Carlo (EMC)

simulated polymerization code

Automized protein embedding into membranes

In this repository, we present a simple procedure to perform Free Energy landscape plots, taking results from molecular dynamics simulation.

A python program for calculating and plotting area-per-lipid and bilayer thickness using GROMACS trajectory files. Uses a script: GridMAT-MD-parallel, originally written by Bevan Lab, Virginia Tech…

The perl scripts for handling pdb files and calculating bond angles, bond lengths, dihedral angles, chainbreaks in main chain atoms, hydrogen bonds and salt bridges between the amino acid chains.

When calculating the protein-ligand complex system, it is necessary to add an appropriate force field to the ligand. One effective method is to use the CGenFF service, but it was found that this fu…