Gromacs

Free Energy Perturbation

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    Gromacs 4.5 now has full support for BAR (Bennett Acceptance Ratio) calculations. There are several new .mdp options controlling simulation output that are described in detail in the manual. The relevant Gromacs tool is g_bar.

    For future releases, we'd like to have support for:

    • MBAR
    • Specifying multiple components of the intermediate state Hamiltonian (lambda).
    • Specifying more than two end states.  
    • Perhaps some mostly automated ways to mutate residues / create A&B states.

    A free energy perturbation tutorial is currently located here: http://www.dillgroup.ucsf.edu/group/wiki/index.php/Free_Energy:_Tutorial, but with the introduction of BAR it's outdated. 

    Page last modified 15:18, 16 Aug 2010 by sander