atoms-ufrj / jctc-lbf-paper

Additional information about the manuscript "A New Formulation for the Concerted Alchemical Calculation of van der Waals and Coulomb Components of Solvation Free Energies".

Additional Information on the LBF Method

This repository contains additional information about the manuscript "A New Formulation for the Concerted Alchemical Calculation of van der Waals and Coulomb Components of Solvation Free Energies". The solvation system of phenol in aqueous media is considered for exemplification. It is attached solvation free energy calculation results and some python scripts applied in molecular dynamics simulations and data post-processing.

Molecular dynamics simulations were performed with OpenMM version 7.5.0 from customizations of the Unified Free Energy Dynamics (UFED) package - https://github.com/craabreu/ufedmm.

The Multistate Bennett Acceptance Ratio (MBAR) method was applied in the data post-processing with the PYMBAR package, which can be friendy manipulated in our analyses with the mics package - https://github.com/craabreu/mics.