Gromacs

An introduction to free energy calculations: Michael Shirts, Session 2A

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    Information will be drawn from the examples on the Alchemistry.org website, including specific GROMACS walkthroughs.For additional powerful analysis tools, download pymbar from https://simtk.org/home/pymbar.  Get the most recent version, updated for GROMACS 4.6.3, by typing:

    svn checkout https://simtk.org/svn/pymbar

    In the directory 'ethanol_solvation'

    You can run a short version of the entire ethanol solvation simulation by running.

    perl run_eth.pl

    You can analyze the existing files ethanol solvation files by typing 

    cd ethanol_solvation; python alchemical-gromacs.py -d outputs/dhdls -p ethanol_direct

    You can run the lambda=0 part of the drug binding calculation  short version by running.

    perl run_eth.pl
    
    Page last modified 11:38, 13 Sep 2013 by mrshirts?