GROMACS Tutorial

Free Energy Calculations: Methane in Water

Justin A. Lemkul, Ph.D.
Department of Pharmaceutical Sciences
University of Maryland, Baltimore

This tutorial will guide the user through the process of calculating a simple free energy change, the decoupling (i.e. removal) of van der Waals interactions between neutral methane and a box of water. It is an updated version of the same tutorial written by David Mobley that I found extremely useful. Due to a substantial number of code changes between the GROMACS version used therein (3.3.1) and present versions (including differences in topology handling, .mdp settings, and data analysis), I think it poignant to provide an updated workflow here.

This tutorial requires a minimum GROMACS version of 5.0. Due to major changes in the way the free energy options are handled, any version prior to 5.0 will not work.

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Looking for the old version? Click here. Please note that the old version will be removed in the near future.

These tutorials were originally written while I was a member of Dr. David Bevan's research group at Virginia Tech.

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