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monolithic simulation programs that are commonly used for biomolecules. Its principal advantages are (1) easy extension and combination with other libraries due to modular library design, (2) a single high-level general-purpose programming language (Python) is used for library implementation as well as for application scripts, (3) use of documented and machine-independent formats for all data files, and (4) interfaces to other simulation and visualization programs.
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The
Molecular Modeling Toolkit is a library that implements common molecular simulation techniques, with an emphasis on biomolecular simulations. It uses modern software engineering techniques (object-oriented design, a high-level language) in order to overcome limitations associated with the large
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As of 28 April 2011, MMTK consists of about 18,000 lines of Python code, 12,000 lines of hand-written C code, and some machine-generated C code.
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visualization using external PDB and VRML viewers; animation of dynamics trajectories and normal modes
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Hinsen K (2000). "The
Molecular Modeling Toolkit: A New Approach to Molecular Simulations".
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the AMBER 94 force field, with several options for handling electrostatic interactions
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construction of molecular systems, with special support for proteins and nucleic acids
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molecular dynamics (with optional thermostat, barostat, and distance constraints)
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infinite systems or periodic boundary conditions (orthorhombic elementary cells)
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10.1002/(SICI)1096-987X(20000130)21:2<79::AID-JCC1>3.0.CO;2-B
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a deformation force field for fast normal mode calculations on proteins
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The
Molecular Modeling Toolkit: A New Approach to Molecular Simulations
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energy minimization (steepest descent and conjugate gradient)
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35:4 January 2000
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Text is available under the Creative Commons Attribution-ShareAlike License. Additional terms may apply.
