Introductory material on molecular simulation and related topics
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Updated
Feb 7, 2018 - TeX
Introductory material on molecular simulation and related topics
A suite of tools to help with molecular simulations/analysis
A validation of A Rehman paper of molecular dynamics.
A tool for removing atoms in IMD config files, just like a cookie cutter in higher dimensions
Calculation of electric-field-based steric (Sterimol) parameters.
Transfer Li ions from cathode to anode in MD simulations
Codes for automating standard VASP and VASP-related calculations.
A development version of GROMACS with extra feature branches by Molecular Biomechanics (MBM) group at HITS.
Code for my PhD level molecular simulations class at Ohio University (CHE 7120)
A library for modular HOOMD-Blue workflows
Welcome to the Lab! Let's Advance the chemical sciences with molecular simulations. 🧪
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.
Molecular modelling of NH4F nanoclusters
Python package for commonly used molecular simulation functions.
Permutationally invariant networks for enhanced sampling (PINES)
Virtual chemistry simulation in 2D based on numpy and numba.
PaCS-MD (Parallel cascade selection molecular dynamics)
Codebase of the paper "Str2Str: A Score-based Framework for Zero-shot Protein Conformation Sampling" (ICLR 2024)
Open-source, cross-platform application supporting lattice-based kinetic Monte Carlo simulations in crystalline systems
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