Code Examples

One of the best ways to learn how to use a new tool is to look at examples. The examples given in this manual were adapted from real-life MMTK applications. They are also contained in the MMTK distribution (directory “Examples”) for direct use and modification.

The example molecules, system sizes, parameters, etc., were chosen to reduce execution time as much as possible, in order to enable you to run the examples interactively step by step to see how they work. If you plan to modify an example program for your own use, don’t forget to check all parameters carefully to make sure that you obtain reasonable results.

• Molecular Dynamics examples
  • The file argon.py contains a simulation of liquid argon at constant temperature and pressure.
  • The file protein.py contains a simulation of a small (very small) protein in vacuum.
  • The file restart.py shows how the simulation started in protein.py can be continued.
  • The file solvation.py contains the solvation of a protein by water molecules.

• Monte-Carlo examples
  • The program backbone.py generates an ensemble of backbone configuration (C-alpha atoms only) for a protein.

• Trajectory examples
  • The file snapshot.py shows how a trajectory can be built up step by step from arbitrary data.
  • The file dcd_import.py converts a trajectory in DCD format (used by the programs CHARMM, X-Plor, and NAMD) to MMTK’s format.
  • The file dcd_export.py converts an MMTK trajectory to DCD format (used by the programs CHARMM, X-Plor, and NAMD).
  • The file trajectory_average.py calculates an average structure from a trajectory.
  • The file trajectory_extraction.py reads a trajectory and writes a new one containing only a subset of the original universe.
  • The file view_trajectory.py shows an animation of a trajectory, provided that an external molecule viewer with animation is available.
  • The file calpha_trajectory.py shows how a much smaller C_α-only trajectory can be extracted from a trajectory containing one or more proteins.

• Normal mode examples

• The file modes.py contains a standard normal mode calculation for a small protein.
• The file constrained_modes.py contains a normal mode calculation for a small protein using a model in which each amino acid residue is rigid.
• The file calpha_modes.py contains a normal mode calculation for a mid-size protein using a C_α model and an elastic network model.
• The file harmonic_force_field.py contains a normal mode calculation for a protein using a detailed but still simple harmonic force field.

• Protein examples
  • The file construction.py shows some more complex examples of protein construction from PDB files.
  • The file analysis.py demonstrates a few analysis techniques for comparing protein conformations.

• DNA examples
  • The file construction.py contains the construction of a DNA strand with a ligand.

• Forcefield examples
  • Electric field term
    • A pure Python implementation (rather slow in general, but tolerable for a simple term like this one) is given in Python/ElectricField.py.
    • A more efficient implementation has the evaluation code written in Cython (Cython/MMTK_electric_field.pyx) while the bookkeeping part remains in Python (Cython/ElectricField.py).
  • Harmonic oscillator term
    • A pure Python implementation (rather slow in general, but tolerable for a simple term like this one) is given in Python/HarmonicOscillatorFF.py.
    • A more efficient implementation has the evaluation code written in Cython (Cython/MMTK_harmonic_oscillator.pyx) while the bookkeeping part remains in Python (Cython/HarmonicOscillatorFF.py).

• MPI examples (parallelization)
  • The file md.py contains a parallelized version of solvation.py.

• Molecular Dynamics integrators
  • The file md.py illustrates how Molecular Dynamics integrators can be implemented in Cython.

• Langevin dynamics integrator
  • The files LangevinDynamics.py and MMTK_langevinmodule.c implement a simple integrator for Langevin dynamics. It is meant as an example of how to write integrators etc. in C, but of course it can also be used directly.

• Visualization examples

• The file additional_objects.py describes the addition of custom graphics objects to the representation of a molecular system.

• Micellaneous examples
  • The example charge_fit.py demonstrates fitting point charges to an electrostatic potential energy surface.
  • The file construct_from_pdb.py shows how a universe can be built from a PDB file in such a way that the internal atom ordering is compatible. This is important for exchanging data with other programs.
  • The file lattice.py constructs molecules placed on a lattice.
  • The file vector_field.py shows how vector fields can be used in the analysis and visualization of collective motions.