Core Objects¶
This class represents a molecular system. |
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Forces¶
This class implements an interaction between triplets of particles that varies with the angle between them. |
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This class implements an interaction between pairs of particles that varies with the distance between them. |
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This class implements an implicit solvation force using the generalized Kirkwood/Grycuk model. |
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This class implements an interaction at trigonal centers corresponding to the projected in-plane angle bend energy between four particles. |
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This class implements the Amoeba multipole interaction. |
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This class implements the Amoeba out-of-plane bend interaction. |
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This class implements the Amoeba pi-torsion interaction. |
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This class implements the Amoeba stretch-bend interaction. |
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This class implements the Amoeba torsion-torsion interaction. |
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This class models van der Waals forces in the AMOEBA force field. |
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This class implements a nonbonded interaction between pairs of particles typically used along with |
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This class uses the Andersen method to maintain constant temperature. |
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This class implements an interaction between pairs of dihedral angles. |
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This class prevents the center of mass of a |
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This class implements interactions between sets of three particles that depend on the angle between them. |
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This class implements bonded interactions between pairs of particles. |
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This class supports energy functions that depend on collective variables. |
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This class is similar to |
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This class supports a wide variety of bonded interactions. |
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This class implements an “external” force on particles. |
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This class implements complex, multiple stage nonbonded interactions between particles. |
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This class supports a wide variety of energy functions used to represent hydrogen bonding. |
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This class supports a wide variety of nonbonded N-particle interactions, where N is user specified. |
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This class implements nonbonded interactions between particles. |
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This class implements interactions between sets of four particles that depend on the torsion angle between them. |
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This class implements forces that are specific to Drude oscillators. |
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This class implements an implicit solvation force using the GBSA-OBC model. |
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This class implements the Gay-Berne anisotropic potential. |
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This class implements an interaction between groups of three particles that varies harmonically with the angle between them. |
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This class implements an interaction between pairs of particles that varies harmonically with the distance between them. |
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This class implements all nonbonded interactions in the HIPPO force field: electrostatics, induction, charge transfer, dispersion, and repulsion. |
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This class uses a Monte Carlo algorithm to adjust the size of the periodic box, simulating the effect of constant pressure. |
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This class uses a Monte Carlo algorithm to adjust the size of the periodic box, simulating the effect of constant pressure. |
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This is a Monte Carlo barostat designed specifically for membrane simulations. |
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This class implements nonbonded interactions between particles, including a Coulomb force to represent electrostatics and a Lennard-Jones force to represent van der Waals interactions. |
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This class implements an interaction between groups of four particles that varies periodically with the torsion angle between them. |
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This class implements an interaction between groups of four particles that varies with the torsion angle between them according to the Ryckaert-Bellemans potential. |
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This is a force whose energy equals the root mean squared deviation (RMSD) between the current coordinates and a reference structure. |
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This class is very similar to |
Integrators¶
These integrators implement an algorithm for advancing the simulation through time.
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This class allows you to use multiple integration algorithms within a single simulation, switching back and forth between them. |
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A base class to encapsulate features common to Drude integrators. |
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This is an error controlled, variable time step |
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This is an error controlled, variable time step |
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Extras¶
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This is a leap-frog Verlet |
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This class defines a chain of Nose-Hoover particles to be used as a heat bath to scale the velocities of a collection of particles subject to thermostating. |
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This class is used for all exceptions thrown by OpenMM. |
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This class represents a three component vector. |
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