GitPlanet

Cheap and reliable Node.js hosting starts at $3/month, and $1/month static HTML hosting

Created with love in Canada, visit hostnodejs.com today

Feel like to post an Ad? Learn Details
All Projects → alchemistry → Alchemlyb

alchemistry / Alchemlyb

Licence: bsd-3-clause
the simple alchemistry library

Programming Languages

python
139335 projects - #7 most used programming language

Labels

librarysciencemolecular-dynamics

Projects that are alternatives of or similar to Alchemlyb

Python Quickui
Scientific One-Liner Interactive GUI Library
Stars: ✭ 153 (+194.23%)
Mutual labels:  library, science
Gromacswrapper
GromacsWrapper is a python package that wraps system calls to Gromacs tools into thin classes. This allows for fairly seamless integration of the gromacs tools (v4.6.x, v5.x, 2016.x, 2018.x, 2019.x, all with the same Python code) into python scripts.
Stars: ✭ 108 (+107.69%)
Mutual labels:  science, molecular-dynamics
Mdanalysis
MDAnalysis is a Python library to analyze molecular dynamics trajectories.
Stars: ✭ 589 (+1032.69%)
Mutual labels:  science, molecular-dynamics
Freud
Powerful, efficient particle trajectory analysis in scientific Python.
Stars: ✭ 118 (+126.92%)
Mutual labels:  science, molecular-dynamics
Stdlib
✨ Standard library for JavaScript and Node.js. ✨
Stars: ✭ 2,749 (+5186.54%)
Mutual labels:  library, science
senpai
Molecular dynamics simulation software
Stars: ✭ 124 (+138.46%)
Mutual labels:  science, molecular-dynamics
Pydhamed
Dynamic Histogram Analysis To Determine Free Energies and Rates from Biased Simulations
Stars: ✭ 17 (-67.31%)
Mutual labels:  science, molecular-dynamics
Kotlin Link Parser
Link preview for android
Stars: ✭ 50 (-3.85%)
Mutual labels:  library
Aiodine
🧪 Async-first Python dependency injection library
Stars: ✭ 51 (-1.92%)
Mutual labels:  library
Libgit2
A cross-platform, linkable library implementation of Git that you can use in your application.
Stars: ✭ 8,208 (+15684.62%)
Mutual labels:  library
Cordova App Harness
[DEPRECATED] Apache Cordova app harness
Stars: ✭ 49 (-5.77%)
Mutual labels:  library
Typescript Lib Example
Example of TypeScript library setup for multiple compilation targets using tsc and webpack
Stars: ✭ 50 (-3.85%)
Mutual labels:  library
Thmap
Concurrent trie-hash map library
Stars: ✭ 51 (-1.92%)
Mutual labels:  library
Sympy
A computer algebra system written in pure Python
Stars: ✭ 8,688 (+16607.69%)
Mutual labels:  science
Hadotnet
🏡 A .NET Standard library for Home Assistant.
Stars: ✭ 52 (+0%)
Mutual labels:  library
Thirtyinch
a MVP library for Android favoring a stateful Presenter
Stars: ✭ 1,052 (+1923.08%)
Mutual labels:  library
Androidsvgloader
Android library for load svg from internet to imageview
Stars: ✭ 52 (+0%)
Mutual labels:  library
Vrac
Declarative html template library from the future. <wip>
Stars: ✭ 52 (+0%)
Mutual labels:  library
Faboptions
A multi-functional FAB component with customizable options
Stars: ✭ 1,060 (+1938.46%)
Mutual labels:  library
Long Shadows
Long Shadows for android!
Stars: ✭ 1,059 (+1936.54%)
Mutual labels:  library
View All Similar Projects ➔

alchemlyb: the simple alchemistry library

|doi| |docs| |build| |cov|

Warning: This library is young. It is not API stable. It is a nucleation point. By all means use and help improve it, but note that it will change with time.

alchemlyb is an attempt to make alchemical free energy calculations easier to do by leveraging the full power and flexibility of the PyData stack. It includes:

  1. Parsers for extracting raw data from output files of common molecular dynamics engines such as GROMACS [Abraham2015]_.

  2. Subsamplers for obtaining uncorrelated samples from timeseries data.

  3. Estimators for obtaining free energies directly from this data, using best-practices approaches for multistate Bennett acceptance ratio (MBAR) [Shirts2008]_ and thermodynamic integration (TI).

In particular, it uses internally the excellent pymbar <http://pymbar.readthedocs.io/>_ library for performing MBAR and extracting independent, equilibrated samples [Chodera2016]_.

.. [Abraham2015] Abraham, M.J., Murtola, T., Schulz, R., Páll, S., Smith, J.C., Hess, B., and Lindahl, E. (2015). GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX 1–2, 19–25.

.. [Shirts2008] Shirts, M.R., and Chodera, J.D. (2008). Statistically optimal analysis of samples from multiple equilibrium states. The Journal of Chemical Physics 129, 124105.

.. [Chodera2016] Chodera, J.D. (2016). A Simple Method for Automated Equilibration Detection in Molecular Simulations. Journal of Chemical Theory and Computation 12, 1799–1805.

.. |doi| image:: https://zenodo.org/badge/68669096.svg :alt: Zenodo DOI :scale: 100% :target: https://zenodo.org/badge/latestdoi/68669096

.. |docs| image:: https://readthedocs.org/projects/alchemlyb/badge/?version=latest :alt: Documentation :scale: 100% :target: http://alchemlyb.readthedocs.io/en/latest/

.. |build| image:: https://travis-ci.org/alchemistry/alchemlyb.svg?branch=master :alt: Build Status :scale: 100% :target: https://travis-ci.org/alchemistry/alchemlyb

.. |cov| image:: https://codecov.io/gh/alchemistry/alchemlyb/branch/master/graph/badge.svg :alt: Code coverage :scale: 100% :target: https://codecov.io/gh/alchemistry/alchemlyb

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].