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Gromacs OPLS-AA/L force field Normal mode calculation

Normally, we recommend using the elastic network model to calculate normal modes for several reasons:

  • It is much faster since the Hessian is calculated analytically
  • It handles missing atoms or broken chains gracefully
  • It does not distort the initial structure with an energy minimization
The most significant drawback is that the eigenfrequencies are arbitrary, since the potentials used are not derived from experiments. If this is important, or if you don't believe us and really want classical force field modes for comparison, we have implemented our fast algorithm in the Gromacs MD package. By using sparse matrix storage we have worked around the classical memory limit, i but since numerical derivation is used to calculate the Hessian it still requires order (N*N) floating-point operations.

Gromacs needs to create an all-atom topology of your input structure, so the chains must be whole and no heavy atoms missing. If your structure is not a simple protein you will probably have to download Gromacs yourself (it's available at Gromacs, but you might have to use the CVS version) and manually edit a topology. Hydrogen atoms will be added, as well as charged termini for proteins.

Since these jobs are quite a bit more taxing on the server compared to the elastic network models, we limit the system size to 5000 atoms and don't run more than 5000 energy minimization steps. If you install Gromacs locally these limitations are obviously no longer an issue.

The results will be returned both as a raw datafile with normal mode vectors, and as a series of PDB movies (structures separated by ENDMDL in a single file). If you load these in a program like PyMol you will get a nice visualization of the mode-induced movements.
To proceed, simply read the trajectory file of a given mode with Pymol, using the File/Open menu options; then assign secondary structures in the Actions menu, then build a cartoon using the Show menu, then Hide the lines, then changes colours using the rainbow option of the Colour palette. Then play the Movie. You can rotate and translate the molecule while it is experiencing NM movements.

BUT: Please, please, please try the Elastic Network version first - it will likely do everything you need without having to worry about these problems :-)




  Marc Delarue http://lorentz.dynstr.pasteur.fr
Page last modified 16:06 March 06, 2006.