Gromacs

Computing potentials of mean force: Justin Lemkul, Session 2A

    Table of contents
    1. 1. Overview
    2. 2. Useful References

    Overview

    This tutorial will cover topics related to the pull code (steered MD) and calculating PMF using umbrella sampling.  Input files (coordinates, .mdp files, and .tpr files) and example data from umbrella sampling will be provided.  The protocol for the tutorial can be found at http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html.  The tutorial session will begin with a short (15-20 minute) presentation on the theory and application of steered MD and umbrella sampling.  Topics will include practical considerations of the tutorial system and we will discuss appropriate settings for more complex systems (protein-ligand systems, molecules partitioning across membranes, etc).  

    Example data are attached below. The tarball includes all input files necessary to run the tutorial (all of which can also be obtained at the tutorial site) in addition to example input and output files from pulling simulations (SMD) and umbrella sampling windows.  The slides used during the tutorial session will be posted to this site no later than Wednesday, Sept. 11.  To maximize the utility of the tutorial session, I would expect that all participants will have (at minimum) read through the tutorial.

    Performing the full workflow will not be possible during the allotted time, as actually performing the simulations would take several hours.  Optimally, participants should have completely worked through the tutorial before attending the workshop session, thus using the time for discussion, questions, and more in-depth assessment of results.

    Though this topic is considered at the beginner/intermediate level, it is expected that all participants will have a working knowledge of GROMACS commands and simple workflows, Linux, and text editors.

     

    Useful References

    Please consider reading some or all of the following papers prior to attending the workshop

    1. Roux, B. (1995) Comp. Phys. Comm. 91: 275.
    2. Kumar, S., Rosenberg, J.M., Bouzida, D., Swendsen, R.H., Kollman, P.A. (1992) J. Comput. Chem. 13: 1011.
    3. Hub, J.S., de Groot, B.L., van der Spoel, D. (2010) J. Chem. Theory Comput. 6: 3713.
    4. Lemkul, J.A. and Bevan, D.R. (2010) J. Phys. Chem. B 114: 1652.
    Page last modified 01:09, 9 Sep 2013 by JLemkul?