/BFEE2_NAMD

Binding free energy simulations with BFEE2

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NAMD_BFEE2

The NAMD_BFEE2 repository includes input and configuration files to perform binding free energy calculation simulations using the BFEE2 method for the 2WI3 system. To install BFEE2, you can follow the steps below:

Installation

First you need to install BFEE2

conda create --name bfee2
conda activate bfee2
conda install -c conda-forge BFEE2

Note that you need to have conda installed on your system for these commands to work.

In addition to installing BFEE2, you also need to install NAMD and Gromacs and patch them with Colvars to run the simulations. The supplimentary Information of the BFEE2 paper titled “Accurate determination of protein:ligand standard binding free energies from molecular dynamics simulations” provides a detailed tutorial on how to install NAMD and Gromacs and patch them with Colvars.