Justin A. Lemkul, Ph.D.
Department of Pharmaceutical Sciences
University of Maryland, Baltimore
This example will guide a new user through the process of setting up a simulation system containing a protein (lysozyme) in a box of water, with ions. Each step will contain an explanation of input and output, using typical settings for general use.
This tutorial assumes you are using a GROMACS version in the 5.x series.
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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