Simple Simulation Engine computational chemistry
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Updated
Jun 9, 2021 - C++
Simple Simulation Engine computational chemistry
GROMACS implementation of PVDF/CNT FF. PVDF from Sahihi et al. , J. Phys. Chem. C 2021 125 (39), 21635-21644, DOI: 10.1021/acs.jpcc.1c05894. CNT from OPLS-AA.
OPLS parameters for perfluoroalkanes in Foyer format. Source: Watkins and Jorgensen, J. Phys. Chem. A, 105, 2001 pp 4118-4125 https://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).
Use main thread to communicate with SQL database and run passed functions on worker threads.
Linear Machine learning Interatomic Potential for atomistic simulations
Analysis scripts for the CHARMM GUI Drude Prepper Paper
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.
MFFS is a mod for Minecraft that adds a modular forcefield system to the game. It is based on the 1.12.2 MFFS mod, but has been completely rewritten for the newer versions of Minecraft.
Classical force-field for peptides containing 4-fluorinated proline residues (or any canonical peptide). Includes a proline ring pucker correction
Nucleic acid labeling and all-atom MD simulations with explicit fluorophores
Modeling the synthesis of SILica materials VIA multiscale computer simulation. (implementation in MARTINI forcefield)
Python-based library for easy force-field fitting
A library for analyzing potential energy surfaces (PESs) and using the resulting PES descriptors for constructing forcefield parameters.
BlockBreakEvent and BlockPlaceEvent is better when canceled!
An implementation of the 3SPN2 and 3SPN2.C coarse-grained DNA forcefields in OpenMM
Bayesian tools for fitting molecular mechanics torsion parameters to quantum chemical data.
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