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azplugins

A HOOMD-blue component for soft matter simulations.

cgpolyelectrolyte

colcryanalysis

Analysis of colloidal crystal structures and their energetics based on radial distribution functions for all i-j pairs in each crystal. Rankings are based on user-defined pair potentials (Hamiltonian) which reflect their relative stabilities in the ground state (T = 0) limit.

colloid_char

Framework for characterizing colloidal self-assembly system states

crayon

dash-public

A GPU-accelerated molecular dyanmics engine controlled through a powerful python interface

deepchem

Democratizing Deep-Learning for Drug Discovery, Quantum Chemistry, Materials Science and Biology

dnacc

Python module for calculating DNACC interaction potentials and binding details

fhmcanalysis

Analysis of Flat Histogram Monte Carlo Simulations. Enables thermodynamic calculations such as bulk properties, phase equilibria, histogram reweighting, and histogram extrapolation.

force_fields

Force fields in various formats

gromacs

Public/backup repository of the gromacs molecular simulation toolkit

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, and 2016.x, all with the same Python code) into python scripts. This is generally superior to shell scripts because of python’s better error handling and superior data structures. It also allows for modularization and code re-use. In addition, commands, warnings and errors are logged to a file so that there exists a complete history of what has been done.

lammps

Public development project of the LAMMPS MD software package

mcdiff

Monte Carlo method to obtain diffusion constants

msmbuilder

:building_construction: Statistical models for biomolecular dynamics :building_construction:

plumed2

Development version of plumed 2

pycsanalysis

pyemma

Python API for Emma's Markov Model Algorithms

pyfeasst

Example implementations of python interface for FEASST

ssages-public

Public release of SSAGES

stokesdt

Stokesian/Brownian Dynamics Simulation Toolkit