Justin A. Lemkul, Ph.D.
Department of Pharmaceutical Sciences
University of Maryland, Baltimore
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 5.0 or newer.
Please note that the purpose of this tutorial is instructional, to build a membrane protein system, and also to understand GROMACS force field organization and methods for modification. This approach works well in the case where one needs to augment a parameter set with other parameters that have been derived in a consistent manner. Some force fields include everything you need. For instance, it is unwise to try to literally follow this approach for a force field like CHARMM36, as it needs no modification. In that case, you are much better off building the system with CHARMM-GUI.
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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