GROMACS Tutorial

Virtual Sites

Justin A. Lemkul, Ph.D.
Department of Pharmaceutical Sciences
University of Maryland, Baltimore

This example will guide a new user through the process of building a linear molecule using virtual sites. The tutorial assumes the user is familiar with basic GROMACS workflows and topology organization.

This tutorial assumes you are using GROMACS version 5.0 or newer. Older (pre-4.5) versions of GROMACS will not work with the example shown here due to changes to the topology format and nomenclature.

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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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