Justin A. Lemkul, Ph.D.
Department of Biochemistry
This example will guide a new user through the process of setting up a simulation system containing two proteins in a box of water, with ions. This tutorial assumes the user has already completed the Lysozyme tutorial or some other introductory GROMACS instructional material. This example is intended to demonstrate how to construct a system of two proteins in a box of water with some arbitrary orientation. There are three cases where two proteins may be present in the unit cell:
This tutorial is not intended to be applicable to multimeric protein structures (case #3 above), since GROMACS can handle multiple chains with no special preparation required. Please consult the manual for proper use of
This tutorial assumes you are using a GROMACS version in the 4.5.x series.
THIS TUTORIAL IS UNDER CONSTRUCTION. PLEASE DO NOT USE IT YET.
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