molecular-mechanics

There are 1 repository under molecular-mechanics topic.

openforcefield / openff-toolkit
The Open Forcefield Toolkit provides implementations of the SMIRNOFF format, parameterization engine, and other tools. Documentation available at http://open-forcefield-toolkit.readthedocs.io
molecular-dynamics force-fields openmm amber chemical-environment-perception smirnoff-force-field molecular-mechanics nsf-grant-che-1738979 open-force-field-consortium forcefield forcefield-parameterization
Language:Python 298
TinkerTools / tinker
Tinker: Software Tools for Molecular Design
molecular-dynamics molecular-mechanics force-fields biomolecular-simulation molecular-modeling
Language:Fortran 124
theochem / iodata
Python library for reading, writing, and converting computational chemistry file formats and generating input files.
quantum-chemistry quantum-chemistry-programs quantum-chemistry-packages computational-chemistry computational-biology computational-physics file-format-converter data-parsing json-schema theoretical-chemistry molecular-mechanics molecular-dynamics molecular-simulation input-output file-formats file-format-library molecular-dynamics-simulation file-conversion file-converter molecular-electronic-structure
Language:Python 120
shirtsgroup / physical_validation
Physical validation of molecular simulations
physical-validation molecular-simulation molecular-dynamics molecular-mechanics python
Language:Python 55
TinkerTools / tinker9
Tinker9: Next Generation of Tinker with GPU Support
molecular-dynamics molecular-mechanics force-fields biomolecular-simulation molecular-modeling gpu-computing
Language:C++ 48
ericchansen / q2mm
Quantum to Molecular Mechanics (Q2MM)
force-fields optimal-parameters force-field-optimization schrodinger quantum molecular-mechanics
Language:Python 21
nlesc-nano / CAT
A collection of tools designed for the automatic construction, and subsequent analysis, of chemical compounds.
automation chemistry molecular-mechanics python quantum-mechanics science scientific-workflows
Language:Python 16
wehs7661 / boltzmann_generators
A repository for the final project implementing/applying Boltzmann generators for Computational Statistical Physics (PHYS 7810) at CU Boulder
deep-learning flow-based-model free-energy-calculations molecular-mechanics neural-network nvp python statistical-mechanics
Language:Jupyter Notebook 14
mdtools
andthum / mdtools
Scripts to prepare and analyze molecular dynamics simulations
science materials-science computational-science computational-biology computational-chemistry computational-physics molecular-simulation molecular-modeling molecular-mechanics molecular-dynamics molecular-dynamics-simulation trajectory-analysis scripts-collection python-scripts python3 mdanalysis gplv3
Language:Python 10
insilichem / garleek
:arrow_right_hook: QM/MM interfacing in Python :leftwards_arrow_with_hook:
computational-chemistry molecular-mechanics oniom qmmm quantum-chemistry
Language:Python 10
MolSSI / mmelemental
Python implementation of the MMSchema specification. Provides fundamental models for molecular mechanics.
interoperability mmschema molecular-dynamics molecular-mechanics python standards
Language:Python 10
nlesc-nano / auto-FOX
A library for analyzing potential energy surfaces (PESs) and using the resulting PES descriptors for constructing forcefield parameters.
quantum-mechanics science chemistry molecular-mechanics forcefield-parameterization forcefield python
Language:Python 7
2040FBDBIC
UAMCAntwerpen / 2040FBDBIC
This repository contains all the course materials that are used in the "Chemo-informatics and computational drug design" course teaches at the University of Antwerp (Belgium)
cheminformatics computational-chemistry course drug-design drug-discovery glide machine-learning maestro molecular-dynamics molecular-dynamics-simulation molecular-mechanics pharmacophore-modelling python rdkit schrodinger virtual-machine virtual-screening drug-receptor-interaction universiteit-antwerpen
Language:Jupyter Notebook 4
UnixJunkie / MMO
Molecular Mechanics in OCaml
docking ligand molecular-mechanics monte-carlo protein ani-2x universal-force-field ocaml-library ocaml-program
Language:OCaml 4
UnixJunkie / vdW_grid_bench
Van der Waals 3D grid initialization benchmark
computational-chemistry high-performance-computing van-der-waals molecular-mechanics ocaml-program
Language:OCaml 4
flavianowilliams / HICOLM3
Multi-Methods for Molecules and Condensed Systems
molecular-dynamics computational-chemistry condensed-phase-simulations molecular-mechanics molecular-modeling
Language:Fortran 3
cluster-analysis-on-monte-carlo-simulations-of-water-adsorption-on-NaCl-atmospheric-particulate
giocoal / cluster-analysis-on-monte-carlo-simulations-of-water-adsorption-on-NaCl-atmospheric-particulate
Code for the paper "Theoretical Investigation of Inorganic Particulate Matter: The Case of Water Adsorption on a NaCl Particle Model Studied Using Grand Canonical Monte Carlo Simulations" and Bachelor's Thesis "Cluster Analysis on the Results of Molecular Simulation of the Water Adsorption Process on Atmospheric Particulate Models"
scikit-learn clustering computational-chemistry python dbscan molecular-mechanics particulate-matter pdb
Language:Python 3
MolSSI / mmic
Molecular Mechanics Interoperable Components
molecular-mechanics pipelines standards interoperability workflows
Language:Python 3
abelcarreras / gromorg
A python GROMACS interface for MD simulations of organic molecular crystals
gromacs molecular-dynamics molecular-mechanics python simulation
Language:Python 2
MolSSI / mmic_optim_gmx
Tactic MMIC for energy optimization using gmx
gmx gromacs energy-minimization mmic-optim python interoperability mmic molecular-mechanics optimization
Language:Python 2
andthum / transfer_Li
Transfer Li ions from cathode to anode in MD simulations
bash-scripts computational-science gromacs materials-science mdanalysis molecular-dynamics molecular-dynamics-simulation molecular-mechanics molecular-modeling molecular-simulation python-scripts science scientific-computing
Language:Shell 1
cchandre / OCDM
Optical Centrifuge for Diatomic Molecules
python3 hamiltonian amo molecular-mechanics numpy scipy sympy matplotlib symplectic-integrators
Language:Python 1
MolSSI / mmic_openff
Tactic MMIC translator for OpenFF/MMSchema
mmschema standards openforcefield smirnoff-force-field forcefield-parameterization interoperability molecular-mechanics mmic
Language:Python 1
MolSSI / mmic_parmed
Tactic MMIC translator for ParmEd/MMSchema
standards molecular-dynamics molecular-mechanics interoperability mmelemental mmschema parmed
Language:Python 1
MolSSI / mmschema
A specification for particle & molecular mechanics
standards molecular-mechanics json-schema hdf5-format hdf5-file-schema interoperability
Language:Python 1
nlesc-nano / Tutorials
A collection of tutorials for the analysis of nanocrystals.
documentation chemistry science quantum-mechanics molecular-mechanics automation
Language:Python 1
NYXFLOWER / DrugDiscovery
An explainable inductive learning model on gene regulatory and toxicogenomic knowledge graph (under development...)
drug-design drug-discovery drug-repurposing explainable-ml gene-regulatory-networks gnn heterogeneous-graph inductive-learning knowledge-graph molecular-mechanics new-dataset predictive-models systems-biology
Language:Jupyter Notebook 1
phatdatnguyen / HCMUTE_Cheminformatics
Cheminformatics course at HCMUTE.
cheminformatics chemistry deep-learning density-functional-theory machine-learning molecular-dynamics molecular-mechanics quantum-chemistry
Language:Jupyter Notebook 1
ryanmrichard / ForceManII
MM code for QM people
force-fields qm-mm computational-chemistry quantum-chemistry molecular-mechanics quantum-mechanics
Language:C++ 1
andthum / lintf2_ether_ana_postproc
Analysis postprocessing utilities for my molecular dynamics simulations of LiTFSI-Ether mixtures
computational-science gromacs materials-science mdanalysis mdtools molecular-dynamics molecular-dynamics-simulations molecular-mechanics molecular-modeling molecular-simulation numpy python-scripts science scientific-computing scipy trajectory-analysis analysis-postprocessing
Language:Python 0
TarekMebrouk / molecular_isomorphism
Retrieve the molecules from the ChEBI site, and parse them and extract the information important for the execution of the Nauty mckay algorithm.
algorithms bioinformatics graph-algorithms isomorphism molecular-mechanics molecular-modeling molecular-structures optimization
Language:Python 0
MolSSI / mmic_ffpa_gmx
Tactic MMIC for force field parameter assignment with gmx
gmx force-field python mmschema mmic interoperability molecular-mechanics molssi gromacs parameterization
Language:Python
MolSSI / mmic_mda
Tactic MMIC translator for MDAnalysis/MMSchema
interoperability mdanalysis mmelemental mmschema molecular-dynamics molecular-mechanics standards
Language:Python
MolSSI / mmic_optim
Strategy MMIC for energy optimization
mmic interoperability molecular-mechanics optimization energy-minimization standards
Language:Python
MolSSI / mmic_qcschema
Tactic MMIC translator for QCSchema/MMSchema
qcschema mmschema interoperability standards converters molecular-mechanics quantum-mechanics qcelemental mmelemental molecular-dynamics quantum-chemistry
Language:Python
MolSSI / mmic_translator
Strategy MMIC translator for MMSchema
conversion interoperability mmic mmschema molecular-mechanics schema standards
Language:Python