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algorithm-archive

A collaborative book on algorithms

ase_ani

ANI-1 neural net potential with python interface (ASE)

awesome-molecular-dynamics

:sunglasses: A curated list of awesome Molecular Dynamics libraries, tools and software.

biostructures.jl

A julia package to read, write and manipulate macromolecular structures (particularly proteins)

chemiinformatics_work

Work based with RDKit and Tensorflow/Theano/Keras etc

cnt-martini

Generates Martini models for open carbon nanotubes to use with Gromacs.

csg-tutorials

coarse-graining tutorials

data_engineering_sample

dataviz-with-python-and-js

The accompanying files for the book 'Dataviz with Python and JavaScript'

deepmd-kit

A deep learning package for many-body potential energy representation and molecular dynamics

demo_dbt

doing_bayesian_data_analysis

Python/PyMC3 versions of the programs described in Doing bayesian data analysis by John K. Kruschke

elba

Blogging and tutorials on how to setup, run and analyse simulations with the Elba and Elba/AA force fields

elba-lammps

Automatically exported from code.google.com/p/elba-lammps

elki

ELKI Data Mining Toolkit

emacs-jedi-direx

Tree style source code viewer for Python buffer

examples

Fortran and Python examples to accompany the book "Computer Simulation of Liquids" by Michael P. Allen and Dominic J. Tildesley (2nd edition, Oxford University Press, 2017). Use the "Clone or download" button, or follow the "...releases" link below.

functional_haskell

Haskell work

genmd

generation scripts for molecular dynamics initial conditions

getcontacts

Library for computing dynamic non-covalent contact networks in proteins throughout MD Simulation

gfk_assignment

GFK Assignment

gro2lam

Gromacs to Lammps simulation converter

laml

Legal Agreement Markup Language

lecturenotes

Lectures on Stochastic Thermodynamics (Chem220b)

md_methods-and-analysis

Repository for MD methods and analysis from submitted or published work

mdanalysis

MDAnalysis is a Python library to analyze molecular dynamics trajectories.

mdanalysis-coarsegraining

An attempt at making a special subtype of MDAnalysis.Universe which allows a mapping scheme to be applied on the fly to an atomistic trajectory.

mdnppackage

mpitutorial

MPI programming lessons in C and executable code examples

nanoparticle_optimization

NanoOpt: Deriving potentials for coarse-grained nanoparticles via potential-matching