A project (and object) for storing, manipulating, and converting molecular mechanics data.
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Updated
Jul 23, 2024 - Python
A project (and object) for storing, manipulating, and converting molecular mechanics data.
Use main thread to communicate with SQL database and run passed functions on worker threads.
The Open Forcefield Toolkit provides implementations of the SMIRNOFF format, parameterization engine, and other tools. Documentation available at http://open-forcefield-toolkit.readthedocs.io
Python-based library for easy force-field fitting
A physical property evaluation toolkit from the Open Forcefield Consortium.
Nucleic acid labeling and all-atom MD simulations with explicit fluorophores
Fragment molecules for quantum mechanics torsion scans
An implementation of the 3SPN2 and 3SPN2.C coarse-grained DNA forcefields in OpenMM
A library for analyzing potential energy surfaces (PESs) and using the resulting PES descriptors for constructing forcefield parameters.
A Package for Parametrization of Molecular Mechanics Force Fields
Modeling the synthesis of SILica materials VIA multiscale computer simulation. (implementation in MARTINI forcefield)
Plot individual potential functions that comprise force fields. Ideal for presentations. Includes energy terms for bonds (harmonic), angles (harmonic), proper torsion (periodic cosine), improper torsion (harmonic), van der Waals (Lennard-Jones), electrostatics (Coulomb), and the Morse potential.
OPLS parameters for perfluoroalkanes in Foyer format. Source: Watkins and Jorgensen, J. Phys. Chem. A, 105, 2001 pp 4118-4125 http://dx.doi.org/10.1021/jp004071w
First program for a class in molecular modelling (done in june 2016). Its an implementation of simple Molecular Dynamics for atoms with a possibility to choose from different algorithms (Verlet, VelocityVerlet, Leepfrog) and potentials (Lenard-Jones, SoftWall, min-barrier-bin).
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