Gromacs

Membrane Simulations: Justin Lemkul, Session 1A

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

    Overview

    The membrane simulation tutorial will cover aspects related to simulations of lipid bilayers with and without embedded proteins. A discussion of .mdp settings will be provided and considerable time will be devoted to lipid analysis. The protocol for the tutorial session will come from my existing membrane protein tutorial, found at http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html.  The format of the tutorial session is as follows.  We will begin with a short (15-20 minute) presentation that will provide an overview of force field and protocol considerations, details of the workflow itself, details of how to prepare membrane protein systems (not just the one found in the tutorial), and step-by-step coverage of common (and not-so-common) analysis techniques.  Following this overview, the remainder of the time will be spent performing the workflow and/or analyzing example data (provided for all participants).  Hopefully this time will also be useful in answering questions that I have not anticipated to improve everyone's understanding of the ins and outs of simulating membranes.

    Example data are provided below.  The tarball includes all necessary input files for performing the tutorial (coordinates, topologies, and as an added bonus the complete force field) and sample data (.xtc and .edr) from a short (10-ns) simulation of KALP15 in DPPC.  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. Kandt, C.L., Ash, W.L., and Tieleman, D.P. (2007) Methods 41: 475.
    2. Klauda, J.B. et al. (2010) J. Phys. Chem. B 114: 7830.
    3. Pastor, R.W. and MacKerell Jr., A.D. (2011) J. Phys. Chem. Lett. 2: 1526.
    4. Ulmschneider, J.P. and Ulmschneider, M.B. (2009) J. Chem. Theory Comput. 5: 1803.
    5. Kukol, A. (2009) J. Chem. Theory Comput. 5: 615.
    6. Siu, S.W.I. et al. (2008) J. Chem. Phys. 128: 125103.
    7. Kandasamy, S.K. and Larson, R.G. (2006) Biophys. J. 90: 2326.
    8. Allen, W.J., Lemkul, J.A., and Bevan, D.R. (2009) J. Comput. Chem. 30: 1952.
    Page last modified 23:07, 10 Sep 2013 by JLemkul?