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.
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.
Bevan Lab Homepage
Virginia Tech Homepage
Virginia Tech Biochemistry
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