choderalab / Yank
Licence: mit
An open, extensible Python framework for GPU-accelerated alchemical free energy calculations.
Stars: ✭ 101
Programming Languages
python
139335 projects - #7 most used programming language
Labels
Projects that are alternatives of or similar to Yank
Schnetpack
SchNetPack - Deep Neural Networks for Atomistic Systems
Stars: ✭ 296 (+193.07%)
Mutual labels: molecular-dynamics
Awesome Python Chemistry
A curated list of Python packages related to chemistry
Stars: ✭ 410 (+305.94%)
Mutual labels: molecular-dynamics
Hoomd Tf
A plugin that allows the use of Tensorflow in Hoomd-Blue for GPU-accelerated ML+MD
Stars: ✭ 25 (-75.25%)
Mutual labels: molecular-dynamics
Gdynet
Unsupervised learning of atomic scale dynamics from molecular dynamics.
Stars: ✭ 37 (-63.37%)
Mutual labels: molecular-dynamics
isicle
In silico chemical library engine for high-accuracy chemical property prediction
Stars: ✭ 31 (-69.31%)
Mutual labels: molecular-dynamics
Uammd
A CUDA project for Molecular Dynamics, Brownian Dynamics, Hydrodynamics... intended to simulate a very generic system constructing a simulation with modules.
Stars: ✭ 11 (-89.11%)
Mutual labels: molecular-dynamics
Mcmd
Monte Carlo and Molecular Dynamics Simulation Package
Stars: ✭ 52 (-48.51%)
Mutual labels: molecular-dynamics
Mdanalysis
MDAnalysis is a Python library to analyze molecular dynamics trajectories.
Stars: ✭ 589 (+483.17%)
Mutual labels: molecular-dynamics
Pydhamed
Dynamic Histogram Analysis To Determine Free Energies and Rates from Biased Simulations
Stars: ✭ 17 (-83.17%)
Mutual labels: molecular-dynamics
Pytim
a python package for the interfacial analysis of molecular simulations
Stars: ✭ 38 (-62.38%)
Mutual labels: molecular-dynamics
Mdtraj
An open library for the analysis of molecular dynamics trajectories
Stars: ✭ 317 (+213.86%)
Mutual labels: molecular-dynamics
Coronavirus
[email protected] COVID-19 efforts
Stars: ✭ 1,118 (+1006.93%)
Mutual labels: molecular-dynamics
Qball
Qball (also known as [email protected]) is a first-principles molecular dynamics code that is used to compute the electronic structure of atoms, molecules, solids, and liquids within the Density Functional Theory (DFT) formalism. It is a fork of the Qbox code by Francois Gygi.
Stars: ✭ 33 (-67.33%)
Mutual labels: molecular-dynamics
Colvars
Collective variables module for molecular simulation and analysis programs
Stars: ✭ 99 (-1.98%)
Mutual labels: molecular-dynamics
Loos
LOOS: a lightweight object-oriented structure analysis library
Stars: ✭ 63 (-37.62%)
Mutual labels: molecular-dynamics
Lammps
Public development project of the LAMMPS MD software package
Stars: ✭ 1,019 (+908.91%)
Mutual labels: molecular-dynamics
YANK
An open, extensible Python framework for GPU-accelerated alchemical free energy calculations
Documentation
Documentation, tutorials, and best practices can be found at getyank.org.
Getting Started
See the Quickstart instructions.
Examples
Examples are available in the yank-examples repository:
git clone https://github.com/choderalab/yank-examples.git
Maintainers
- Andrea Rizzi
<[email protected]>(WCMC) - Hannah Bruce Macdonald
<hannah.brucemacdonald>(MSKCC) - John D. Chodera
<[email protected]>(MSKCC) - Levi N. Naden
<[email protected]>(MSKCC)
Contributors
- Kim Branson (Stanford)
- Kyle A. Beauchamp (MSKCC)
- Peter M. Eastman (Stanford)
- Mark Friedrichs (Stanford)
- Imran Haque (Stanford)
- Patrick B. Grinaway (MSKCC)
- Christoph Klein (University of Virginia)
- Rosa Luirink (VU Amsterdam)
- Daniel L. Parton (MSKCC)
- Randy Radmer (Stanford)
- Arien Sebastian Rustenburg (MSKCC)
- Michael Shirts (University of Colorado Boulder)
- Kai Wang (University of Virginia)
Note that the project description data, including the texts, logos, images, and/or trademarks,
for each open source project belongs to its rightful owner.
If you wish to add or remove any projects, please contact us at [email protected].