Tutorial Gromacs 4 5 3
Revision as of 08:26, 5 July 2011 by Michael Shirts (talk | contribs) (Created page with "== <font size="+3" color="0000FF">GROMACS Tutorial</font> == === <font size="+2" color="0000FF">Free Energy Calculations: Methane in Water</font> === '''Justin Lemkul'''<br /> ...")
GROMACS Tutorial
Free Energy Calculations: Methane in Water
Justin Lemkul
Department of Biochemistry, Virginia Tech
[[Image:./Images/system.png]]
|
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]] |