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

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

    svn checkout

    In the directory 'ethanol_solvation'

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


    You can analyze the existing files ethanol solvation files by typing 

    cd ethanol_solvation; python -d outputs/dhdls -p ethanol_direct

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

    Page last modified 11:38, 13 Sep 2013 by mrshirts?