Gromacs

Topology preparation, "What's in a log file", basic performance improvements: Mark Abraham, Session 1A

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    Version as of 14:33, 30 Nov 2021

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    Contents

    This tutorial comes in two parts. In the first, we will look at setting up an implicit solvent simulation on a medium-sized peptide. Later, we will learn how to look at the log file produced by mdrun, and learn some of what was going on in our simulation. This tutorial is intended for use with GROMACS 4.6.3. You may see minor differences if you use other versions of GROMACS.

    The text of the tutorial is available in PDF format. This gzip-ed tar archive of the input files will also be needed to work along with the tutorial.

    Page last modified 21:34, 9 Sep 2013 by mabraham