GitHub topics: openmm
openforcefield/openff-interchange
A project (and object) for storing, manipulating, and converting molecular mechanics data.
Language: Python - Size: 6.35 MB - Last synced at: 1 day ago - Pushed at: 1 day ago - Stars: 75 - Forks: 24
huichenggong/GrandFEP
Alchemical Free Energy Calculations with Grand Canonical Ensemble
Language: Python - Size: 12 MB - Last synced at: 1 day ago - Pushed at: 1 day ago - Stars: 1 - Forks: 0
AspirinCode/awesome-AI4MolConformation-MD
List of molecules (small molecules, RNA, peptide, protein, enzymes, antibody, and PPIs) conformations and molecular dynamics (force fields) using generative artificial intelligence and deep learning
Size: 4.45 MB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 184 - Forks: 17
cabb99/open3spn2
An implementation of the 3SPN2 and 3SPN2.C coarse-grained DNA forcefields in OpenMM
Language: Python - Size: 32.9 MB - Last synced at: 11 days ago - Pushed at: 11 days ago - Stars: 18 - Forks: 8
choderalab/openmmtools
A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine.
Language: Python - Size: 33 MB - Last synced at: 13 days ago - Pushed at: 13 days ago - Stars: 271 - Forks: 85
SSAGESLabs/PySAGES
Python Suite for Advanced General Ensemble Simulations
Language: Python - Size: 59.4 MB - Last synced at: 8 days ago - Pushed at: 8 days ago - Stars: 79 - Forks: 27
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
Language: Python - Size: 218 MB - Last synced at: 14 days ago - Pushed at: 14 days ago - Stars: 339 - Forks: 97
openforcefield/openff-evaluator
A physical property evaluation toolkit from the Open Forcefield Consortium.
Language: Python - Size: 17.3 MB - Last synced at: 14 days ago - Pushed at: 14 days ago - Stars: 56 - Forks: 19
quantaosun/Ambertools-OpenMM-MD
Open Source, Mostly just clicking mouse to finish a simulation with Ambertools and OpenMM. It was designed to use locally but another notebook to finish the simulaiton on Colab was attached as well.
Language: Jupyter Notebook - Size: 14.9 MB - Last synced at: 17 days ago - Pushed at: 17 days ago - Stars: 34 - Forks: 6
shirtsgroup/cg_openmm
Tools to build coarse grained models and perform simulations with OpenMM
Language: Python - Size: 395 MB - Last synced at: 2 days ago - Pushed at: over 2 years ago - Stars: 23 - Forks: 8
choderalab/perses
Experiments with expanded ensembles to explore chemical space
Language: Python - Size: 42.9 MB - Last synced at: about 1 month ago - Pushed at: 3 months ago - Stars: 192 - Forks: 50
RedesignScience/cvpack
Useful Collective Variables for OpenMM
Language: Python - Size: 6.68 MB - Last synced at: 22 days ago - Pushed at: about 1 year ago - Stars: 13 - Forks: 1
AspirinCode/AlphaPPImd
Exploring the conformational ensembles of protein-protein complexes with transformer-based generative neural networks
Language: Jupyter Notebook - Size: 7.98 MB - Last synced at: about 1 month ago - Pushed at: 11 months ago - Stars: 28 - Forks: 3
JoaoRodrigues/openmm_scripts
Collection of Python scripts to setup and run simulations with OpenMM
Language: Python - Size: 161 KB - Last synced at: about 1 month ago - Pushed at: almost 5 years ago - Stars: 16 - Forks: 9
Marcello-Sega/pytim
a python package for the interfacial analysis of molecular simulations
Language: Python - Size: 206 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 85 - Forks: 35
scipion-chem/scipion-chem-openmm
Plugin for OpenMM software
Language: Python - Size: 112 KB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 0 - Forks: 0
sunghunbae/mdscribe
A toolset for molecular dynamics
Language: Python - Size: 821 KB - Last synced at: 18 days ago - Pushed at: 2 months ago - Stars: 0 - Forks: 0
giorginolab/miniomm
A simple OpenMM wrapper for common-case MD runs
Language: Python - Size: 38.1 MB - Last synced at: 17 days ago - Pushed at: 4 months ago - Stars: 5 - Forks: 3
weinsteinlab/OpenMM-Slurm-Ensemble
This repository contains the scripts/workflow components needed to launch arbitrarily large ensembles of molecular dynamics simulations with openMM (with GPUs), submitting jobs to Slurm.
Language: Rich Text Format - Size: 38.9 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 3 - Forks: 0
insilichem/ommprotocol
A command line application to launch molecular dynamics simulations with OpenMM
Language: Python - Size: 1.42 MB - Last synced at: 19 days ago - Pushed at: about 3 years ago - Stars: 40 - Forks: 8
cbc-univie/transformato
Set up relative free energy calculations using a common scaffold
Language: Python - Size: 209 MB - Last synced at: 22 days ago - Pushed at: 22 days ago - Stars: 22 - Forks: 6
matsunagalab/md_inputs
Place of learning OpenMM
Language: Rich Text Format - Size: 90.5 MB - Last synced at: 2 months ago - Pushed at: 6 months ago - Stars: 0 - Forks: 0
essex-lab/grand
A Python module for carrying out GCMC insertions and deletions of water molecules in OpenMM.
Language: Python - Size: 1.84 MB - Last synced at: 6 months ago - Pushed at: almost 2 years ago - Stars: 60 - Forks: 19
pol-sb/simul-protein-small-molecule
Tools to study LLPS in IDP systems using the OpenMM python API
Language: Python - Size: 3.06 MB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 5 - Forks: 0
seekrcentral/seekr2
Simulation-Enabled Estimation of Kinetic Rates - Version 2
Language: Python - Size: 28.4 MB - Last synced at: 2 months ago - Pushed at: 3 months ago - Stars: 27 - Forks: 6
matsunagalab/docker-openmm
dockerfile for openmm
Language: Shell - Size: 14.6 KB - Last synced at: about 1 month ago - Pushed at: almost 5 years ago - Stars: 3 - Forks: 3
John-Kazan/OpenMMScripts
This repository provides scripts for running NPT MD simulations using OpenMM, specifically designed for use on the PHX cluster.
Language: Python - Size: 67.4 KB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0
bbye98/mdhelper 📦
A batteries-included toolkit of analysis modules and helper functions for molecular dynamics (MD) simulations.
Language: Python - Size: 87.8 MB - Last synced at: 9 days ago - Pushed at: about 1 year ago - Stars: 8 - Forks: 0
craabreu/openxps
Extended Phase-Space Simulations with OpenMM
Language: Python - Size: 646 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 3 - Forks: 0
EnglishBeach/MolecularModeling
Part of the diploma.
Language: Jupyter Notebook - Size: 142 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0
pyib/pyib
PyTorch & OpenMM implementations of deep-learning based approaches for learning and biasing reaction coordinates in molecular simulations.
Language: Python - Size: 33.1 MB - Last synced at: about 1 year ago - Pushed at: about 3 years ago - Stars: 0 - Forks: 1
apallath/pyves
Variationally enhanced sampling for single-particle langevin dynamics with neural network bias potentials and path collective variables. Based on OpenMM + PyTorch.
Language: Python - Size: 101 MB - Last synced at: about 1 year ago - Pushed at: almost 3 years ago - Stars: 0 - Forks: 0
choderalab/yank
An open, extensible Python framework for GPU-accelerated alchemical free energy calculations.
Language: Python - Size: 45.3 MB - Last synced at: about 1 year ago - Pushed at: almost 2 years ago - Stars: 171 - Forks: 69
mizu-bai/openmm-state-to-g96
Convert OpenMM state xml to g96 format
Language: Python - Size: 812 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0
choderalab/openmm-tutorials
Quickstart Python tutorials helping molecular dynamics practitioners get up to speed with OpenMM
Language: Jupyter Notebook - Size: 1.34 MB - Last synced at: about 1 year ago - Pushed at: over 7 years ago - Stars: 46 - Forks: 16
choderalab/integrator-benchmark
Code for enumerating and evaluating numerical methods for Langevin dynamics using near-equilibrium estimates of the KL-divergence. Accompanies https://doi.org/10.3390/e20050318
Language: Jupyter Notebook - Size: 31.9 MB - Last synced at: about 1 year ago - Pushed at: about 7 years ago - Stars: 11 - Forks: 3
mizu-bai/openmm-g96-reporter
G96 format based reporter for OpenMM
Language: Python - Size: 5.27 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0
leelasd/OPLSAA-DB
Database of hand-built OPLS-AA parameters and topologies for 464 molecules. Zip files contains parameter and topologies for OpenMM, Gromacs, NAMD, CHARMM, LAMMPS, TINKER, CNS/X-PLOR, Q, DESMOND, BOSS and MCPRO.
Size: 7.28 MB - Last synced at: about 1 year ago - Pushed at: almost 7 years ago - Stars: 31 - Forks: 7
fahbench/fahbench
Folding@home GPU benchmark
Language: C++ - Size: 19.6 MB - Last synced at: about 1 year ago - Pushed at: over 2 years ago - Stars: 33 - Forks: 9
RedesignScience/openmm-cpp-forces
Platform-agnostic OpenMM Forces
Language: C++ - Size: 833 KB - Last synced at: about 2 months ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 1
oess/oeommtools
Tool collection to integrate and mix OpenEye and OpenMM
Language: Python - Size: 15.1 MB - Last synced at: over 1 year ago - Pushed at: almost 2 years ago - Stars: 12 - Forks: 2
SimonBoothroyd/absolv
Absolute solvation free energy calculations with OpenFF and OpenMM
Language: Python - Size: 3.76 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 11 - Forks: 2
craabreu/ufedmm
Unified Free Energy Dynamics (UFED) simulations with OpenMM
Language: Python - Size: 2.08 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 21 - Forks: 9
YevChern/sanxs-force
Restrained ensemble molecular dynamics method implementation for small angle scattering data.
Language: C++ - Size: 13.7 MB - Last synced at: over 1 year ago - Pushed at: over 4 years ago - Stars: 1 - Forks: 0
choderalab/saltswap
Package to fluctuate the number of counterions in an OpenMM simulation
Language: Jupyter Notebook - Size: 7.87 MB - Last synced at: about 1 year ago - Pushed at: over 3 years ago - Stars: 6 - Forks: 3
timbernat/polysaccharide
Polymer-Oriented Library Yielding Structure Assignment, Calculation of CHARges, Interchange, and Data Elucidation
Language: Python - Size: 342 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 1
Hekstra-Lab/mdtools
Tools for running MD simulations in OpenMM
Language: Python - Size: 253 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 5 - Forks: 3
choderalab/iapetus
Open source toolkit for predicting bacterial porin permeation
Language: Python - Size: 3.21 MB - Last synced at: about 1 year ago - Pushed at: over 3 years ago - Stars: 2 - Forks: 2
Gallicchio-Lab/openmm_agbnp_plugin
An OpenMM plugin implementing the AGBNP implicit solvent model
Language: C++ - Size: 5.59 MB - Last synced at: almost 2 years ago - Pushed at: over 5 years ago - Stars: 4 - Forks: 1
SSAGESLabs/openmm-dlext
Plugin for OpenMM providing simulation data wrappers as DLPack data structures
Language: C++ - Size: 129 KB - Last synced at: almost 2 years ago - Pushed at: almost 3 years ago - Stars: 1 - Forks: 4
smlee99/InteractionGroup
Energy decomposition module for the analysis of molecular dynamics trajectories
Language: Python - Size: 434 KB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 2 - Forks: 0
atoms-ufrj/atomsmm
AtomsMM is an OpenMM customization for the ATOMS group at UFRJ/Brazil
Language: Python - Size: 722 KB - Last synced at: over 1 year ago - Pushed at: about 5 years ago - Stars: 7 - Forks: 4
mrat1618/ff-conversion-openmm
Force field conversion utility: Tinker, LAMMPS and Antechamber parameters to OpenMM XML
Language: Python - Size: 7.81 KB - Last synced at: almost 2 years ago - Pushed at: about 4 years ago - Stars: 0 - Forks: 0
Gallicchio-Lab/openmm_sdm_workflow
Example of the use of the single-decoupling method setup workflow
Language: Python - Size: 901 KB - Last synced at: almost 2 years ago - Pushed at: about 4 years ago - Stars: 1 - Forks: 3
rajatkrpal/openmm_sdm_plugin
OpenMM plugin to implement single-decoupling method in alchemical free energy calculations
Language: C++ - Size: 1.41 MB - Last synced at: almost 2 years ago - Pushed at: about 4 years ago - Stars: 5 - Forks: 3
choderalab/mpiplus
Utilities to run on MPI.
Language: Python - Size: 63.5 KB - Last synced at: about 1 year ago - Pushed at: about 2 years ago - Stars: 3 - Forks: 1
atoms-ufrj/playmol
Playmol is a(nother) software for building molecular models
Language: Fortran - Size: 1.78 MB - Last synced at: over 1 year ago - Pushed at: about 2 years ago - Stars: 14 - Forks: 5
msultan/SML_CV
Using supervised machine learning to build collective variables for accelerated sampling
Language: Jupyter Notebook - Size: 140 MB - Last synced at: about 2 years ago - Pushed at: almost 7 years ago - Stars: 22 - Forks: 4
mohebifar/openmm-transformer
A cleaner way to manage custom forces in OpenMM
Language: Python - Size: 3.91 KB - Last synced at: 10 days ago - Pushed at: over 5 years ago - Stars: 4 - Forks: 0
craabreu/openmm_rigidbody_plugin
Rigid Body Dynamics with OpenMM
Language: C++ - Size: 371 KB - Last synced at: about 2 years ago - Pushed at: almost 7 years ago - Stars: 9 - Forks: 1
choderalab/protons
OpenMM testbed for constant-pH methodologies.
Language: Python - Size: 161 MB - Last synced at: about 1 year ago - Pushed at: over 3 years ago - Stars: 20 - Forks: 13
uibcdf/Molecular-Systems
UIBCDF test systems
Language: Python - Size: 52.3 MB - Last synced at: about 2 months ago - Pushed at: about 3 years ago - Stars: 1 - Forks: 1
inspiremd/kinomodel
A tool for modeling different kinase conformations with various ligand binding poses.
Language: Python - Size: 3.1 MB - Last synced at: about 2 years ago - Pushed at: almost 6 years ago - Stars: 5 - Forks: 2
CrayLabs/smartsim-openmm
SmartSim used to implement the DeepDriveMD workflow with OpenMM
Language: Python - Size: 607 KB - Last synced at: over 1 year ago - Pushed at: about 3 years ago - Stars: 7 - Forks: 1
insilichem/tangram_mmsetup
A graphical interface to run OpenMM simulations in UCSF Chimera.
Language: Python - Size: 117 KB - Last synced at: 3 months ago - Pushed at: over 6 years ago - Stars: 2 - Forks: 0
choderalab/saltswap-results
Repository for the results of saltswap that are necessary for a first publication
Language: Jupyter Notebook - Size: 12.9 MB - Last synced at: about 1 year ago - Pushed at: over 7 years ago - Stars: 1 - Forks: 0
Inniag/openmm-journal-club
:notebook: Overview the OpenMM Molecular Dynamics Engine
Language: Jupyter Notebook - Size: 369 KB - Last synced at: about 2 years ago - Pushed at: about 6 years ago - Stars: 3 - Forks: 1
lambdal/openmm_benchmark
OpenMM benchmark Repo
Language: Python - Size: 2.16 MB - Last synced at: about 2 years ago - Pushed at: about 5 years ago - Stars: 0 - Forks: 1
egallicc/openmm_gaussvol_plugin
A plugin to add Gaussian surface area model to OpenMM
Language: C++ - Size: 4.38 MB - Last synced at: almost 2 years ago - Pushed at: over 6 years ago - Stars: 0 - Forks: 2
choderalab/iapetus-examples
Bacterial porin permeation calculation examples for iapetus
Language: Python - Size: 9.4 MB - Last synced at: about 1 year ago - Pushed at: over 6 years ago - Stars: 0 - Forks: 1
snsinfu/openmm-experiments
Conda environment for C++ development with OpenMM
Language: C++ - Size: 9.77 KB - Last synced at: about 2 years ago - Pushed at: over 7 years ago - Stars: 0 - Forks: 0
