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Molecular Modelling Toolkit 2.2

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Konrad Hinsen

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Jul 4, 2002, 12:19:38 PM7/4/02

Molecular Modeling Toolkit release 2.2
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The Molecular Modelling Toolkit (MMTK) is an Open Source program
library for molecular simulation applications, written in Python with
C modules for time-critical parts. In addition to providing
ready-to-use implementations of standard algorithms, MMTK serves as a
code basis that can be easily extended and modified to deal with
standard and non-standard problems in molecular simulations.

MMTK's functionality includes

- construction of molecular systems, with special support for proteins
and nucleic acids
- infinite systems or periodic boundary conditions (orthorhombic
elementary cells)
- common geometrical operations on coordinates
- rigid-body fits
- visualization using external PDB and VRML viewers; animation of
dynamics trajectories and normal modes
- the AMBER 94 force field, with several options for handling electrostatic
interactions
- a deformation force field for fast normal mode calculations on proteins
- energy minimization (steepest descent and conjugate gradient)
- molecular dynamics (with optional thermostat, barostat, and
distance constraints)
- normal mode analysis
- trajectory operations
- point charge fits
- molecular surface calculations
- interfaces to other programs

Release 2.2 contains numerous small additions, improvements, and
bug fixes. The main new features since the last official release,
2.0, are

- Parallelization on shared-memory machines using threads.
- Parallelization using MPI. The parallelization uses a data replication
scheme and is therefore efficient only for a relatively small number
of processors.
- Various harmonic force fields for efficient normal mode calculations
on proteins.
- Harmonic restraints.
- OPLS force field.
- TrajectoryViewer, a tool for inspecting MMTK trajectories.

For more information and for downloading, see the MMTK Web site at

http://dirac.cnrs-orleans.fr/MMTK/

http://starship.python.net/~hinsen/MMTK/