Normal Mode Analysis

    Normal procedure with GROMACS

    In Normal Mode Analysis (NMA), calculations are run in order to study the underlying, large-scale functional motions of a macromolecule, typically a protein. The calculations require very thorough energy minimization and calculation of a Hessian matrix.

    In general, both for final-stage energy minimization (with L-BFGS) and actual normal mode analysis you can use a setup with

    • double-precision GROMACS installation
    • switched Coulomb & van der Waals interactions; cutoffs e.g. at 1.0 nm, switched from 0.8 nm (or shifted from 0 nm).
    • rlist at 1.2 to 1.3

    It is imperative that you use the -t option to grompp when you create the normal mode run input file, so that you read full precision binary coordinates and not the three-decimal .gro file.



    Page last modified 10:57, 10 Oct 2009 by JLemkul?