FENEB

A tool for performing nudged elastic bands simulations on the free energy surface using Amber.

How it works

Run molecular dynamics with AMBER, feed this code with .rst7 and .nc files, and you will get new .rst7 files to continue the optimization. Additionally, every time this code is executed, an output file will be generated with thermodynamic information.

Using a bash script is recommended for automatization. Check the tutorial folder for examples and a short tutorial!

Requirements

This code requires NETCDF Libraries.

Compilation

Execute

  ./compile_feneb.sh

References

• Semelak, et. al. (2022). Minimum free energy pathways with the nudged elastic band method in combination with a QM-MM Hamiltonian. ChemRxiv. Cambridge: Cambridge Open Engage. This content is a preprint and has not been peer-reviewed.
• Bohner, et. al. (2014). Nudged-elastic band used to find reaction coordinates based on the free energy. The Journal of Chemical Physics, 140(7), 074109.