Molecular mechanics#
MolSysMT provides a unified Pythonic interface for molecular mechanics operations—including potential energy calculations, energy minimizations, atomic force evaluations, and parameter definitions.
Note
Molecular Mechanics Backend Philosophy Unlike other areas of MolSysMT where native algorithms are implemented (such as structural analyses, SASA, contact maps, and visual inspection), molecular mechanics calculations intentionally rely on established, high-performance simulation engines (currently OpenMM by default). MolSysMT standardizes the interaction with these engines, translating topology formats, parameter files, and force field keywords seamlessly.
Calculating mechanical degrees of freedom for parameterized systems |
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Translating force field specifications into engine parameter definitions |
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Extracting atomic force vectors and magnitudes from force fields |
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Calculating non-bonded interaction energies across selections or residue sets |
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Evaluating total potential energy and force field energy components |
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Relaxing molecular structures to local potential energy minima |