Tutorial Gromacs 4 5 3
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GROMACS Tutorial
Free Energy Calculations: Methane in Water
Justin Lemkul
Department of Biochemistry, Virginia Tech
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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 and data analysis), I think it poignant to provide an updated workflow here. This tutorial requires a GROMACS version in the 4.5.x series, preferably 4.5.3. Any version prior to 4.5 will not work. [[./01_theory.html|Start the tutorial!]] [[../index.html|Tutorials Home]] |