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

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    1. 1. Overview

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    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. In the directory in your virtual machine for this tutorial, you will find four directories, each with some files you can use to follow along with the tutorial. If you make a mistake, there's backups of input and output for each stage in the archive subdirectory for each stage. This tutorial assumes you are comfortable using cd to move up and down through the directory hierarchy, and ls to see what you have in the current directory. This tutorial is intended for use with GROMACS 4.6.3. You may see minor differences if you use other versions of GROMACS.

    Page last modified 21:27, 9 Sep 2013 by mabraham