Application Layer¶
Loaders and Setup¶
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AmberInpcrdFile parses an AMBER inpcrd file and loads the data stored in it. |
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AmberPrmtopFile parses an AMBER prmtop file and constructs a Topology and (optionally) an OpenMM System from it. |
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Reads and parses a CHARMM coordinate file (.crd) into its components, namely the coordinates, CHARMM atom types, resname, etc. |
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Stores a parameter set defined by CHARMM files. |
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A chemical structure instantiated from CHARMM files. |
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Reads and parses data, velocities and coordinates from a CHARMM restart file (.rst) of file name ‘fname’ into class attributes |
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DCDFile provides methods for creating DCD files. |
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DesmondDMSFile parses a Desmond DMS (desmond molecular system) and constructs a topology and (optionally) an OpenMM System from it |
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GromacsGroFile parses a Gromacs .gro file and constructs a set of atom positions from it. |
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GromacsTopFile parses a Gromacs top file and constructs a Topology and (optionally) an OpenMM System from it. |
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PDBFile parses a Protein Data Bank (PDB) file and constructs a Topology and a set of atom positions from it. |
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PDBxFile parses a PDBx/mmCIF file and constructs a Topology and a set of atom positions from it. |
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XTCFile provides methods for creating XTC files. |
Representation and Manipulation¶
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Topology stores the topological information about a system. |
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A Chain object represents a chain within a Topology. |
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A Residue object represents a residue within a Topology. |
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An Atom object represents an atom within a Topology. |
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Modeller provides tools for editing molecular models, such as adding water or missing hydrogens. |
Simulation¶
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A ForceField constructs OpenMM System objects based on a Topology. |
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Simulation provides a simplified API for running simulations with OpenMM and reporting results. |
Reporting Output¶
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CheckpointReporter saves periodic checkpoints of a simulation. |
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DCDReporter outputs a series of frames from a Simulation to a DCD file. |
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PDBReporter outputs a series of frames from a Simulation to a PDB file. |
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PDBxReporter outputs a series of frames from a Simulation to a PDBx/mmCIF file. |
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StateDataReporter outputs information about a simulation, such as energy and temperature, to a file. |
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XTCReporter outputs a series of frames from a Simulation to a XTC file. |
Extras¶
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A collective variable that can be used to bias a simulation with metadynamics. |
For non-fatal PSF parsing issues |
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An Element represents a chemical element. |
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Performs metadynamics. |
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SimulatedTempering implements the simulated tempering algorithm for accelerated sampling. |
Units¶
A physical dimension such as length, mass, or temperature. |
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Physical unit expressed in exactly one BaseDimension. |
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Physical quantity, such as 1.3 meters per second. |
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ScaledUnit is like a BaseUnit, but it is based on another Unit. |
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Unit prefix that can be multiplied by a unit to yield a new unit. |
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Physical unit such as meter or ampere. |
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A complete system of units defining the base unit in each dimension |