GROMACS Tutorial

KALP15 in DPPC

Justin Lemkul
Department of Biochemistry, Virginia Tech


This tutorial will guide the user through the preparation and simulation of a simple membrane protein, in this case KALP15, in a model membrane, DPPC. The tutorial assumes the user has already successfully completed the Lysozyme tutorial, some other tutorial, or is otherwise well-versed in GROMACS simulation methods and topology organization. The level of detail in this tutorial will be focused on membrane protein-specific considerations, and will not provide an exhaustive explanation of every step, as with the Lysozyme tutorial.

This tutorial assumes you are using GROMACS version 4.5.3 or newer. Many of the filenames, command line options, and other assorted details will be very different if you attempt to use a pre-4.5 version of GROMACS.


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