#
openmm
Here are 45 public repositories matching this topic...
An open, extensible Python framework for GPU-accelerated alchemical free energy calculations.
python
molecular-dynamics
openmm
molecular-dynamics-simulation
drug-discovery
free-energy
free-energy-perturbation
alchemical-free-energy-calculations
mskcc
alchemical
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Updated
Nov 15, 2020 - Python
A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine.
python
molecular-dynamics
openmm
molecular-simulations
mcmc
markov-chain-monte-carlo
alchemical-free-energy-calculations
free-energy-calculations
replica-exchange
integrators
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Updated
Jul 8, 2021 - Python
Experiments with expanded ensembles to explore chemical space
python
simulation
molecular-dynamics
openmm
molecular-design
free-energy-perturbation
expanded-ensembles
relative-free-energy
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Updated
Aug 7, 2021 - Python
a python package for the interfacial analysis of molecular simulations
python
molecular-dynamics
openmm
scientific-computing
data-analysis
lammps
charmm
simulations
molecular-simulations
namd
gromacs
interfaces
mdanalysis
mdtraj
willard-chandler
interfacial-atoms
sasa
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Updated
Apr 21, 2021 - Python
A physical property evaluation toolkit from the Open Forcefield Consortium.
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Updated
Aug 4, 2021 - Python
Quickstart Python tutorials helping molecular dynamics practitioners get up to speed with OpenMM
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Updated
Aug 26, 2017 - Jupyter Notebook
A command line application to launch molecular dynamics simulations with OpenMM
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Updated
Jun 18, 2021 - Python
Using supervised machine learning to build collective variables for accelerated sampling
machine-learning
openmm
supervised-learning
enhanced-sampling
plumed
supervised-machine-learning
metadynamics
collective-variables
accelerated-sampling
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Updated
Jun 26, 2018 - Jupyter Notebook
OpenMM testbed for constant-pH methodologies.
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Updated
Jan 5, 2020 - Python
A Python module for carrying out GCMC insertions and deletions of water molecules in OpenMM.
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Updated
Jun 15, 2021 - Python
An implementation of the 3SPN2 and 3SPN2.C coarse-grained DNA forcefields in OpenMM
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Updated
Jun 10, 2021 - Python
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.
molecular-dynamics
openmm
molecular-simulation
thermodynamics
lammps
charmm
force-field
namd
gromacs
tinker
opls-aa
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Updated
Aug 2, 2018
Playmol is a(nother) software for building molecular models
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Updated
Jun 1, 2021 - Fortran
Tool collection to integrate and mix OpenEye and OpenMM
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Updated
Jul 15, 2021 - Python
Collection of Python scripts to setup and run simulations with OpenMM
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Updated
May 22, 2020 - Python
Tools to build coarse grained models and perform simulations with OpenMM
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Updated
Aug 4, 2021 - Python
AtomsMM is an OpenMM customization for the ATOMS group at UFRJ/Brazil
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Updated
Apr 11, 2020 - Python
An OpenMM plugin implementing the AGBNP implicit solvent model
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Updated
Oct 26, 2019 - C++
A tool for modeling different kinase conformations with various ligand binding poses.
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Updated
Aug 5, 2019 - Python
Package to fluctuate the number of counterions in an OpenMM simulation
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Updated
Dec 2, 2017 - Jupyter Notebook
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
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Updated
Mar 28, 2018 - Jupyter Notebook
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Updated
May 3, 2019 - Jupyter Notebook
Python Suite for Advanced General Ensemble Simulations
python
openmm
enhanced-sampling
gpu-support
collective-variables
hoomd-blue
scientific-machine-learning
miccom
pysages
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Updated
Aug 6, 2021 - Python
OpenMM plugin to implement single-decoupling method in alchemical free energy calculations
molecular-dynamics
openmm
alchemical-free-energy-calculations
openmm-plugin
single-decoupling-method
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Updated
Apr 22, 2021 - C++
Tools for running MD simulations in OpenMM
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Updated
Jun 14, 2021 - Python
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