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analysis

Analysis scripts for molecular dynamics simulations of stratum corneum lipid multilayers.

antefoyer

Antechamber plugin to foyer and support for the GAFF forcefield

bayesian-stats-modelling-tutorial

How to do Bayesian statistical modelling using numpy and PyMC3

cg_bond_calculator

Calculates bonded interactions from atomistic-to-CG mapped trajectories

cg_mapping

Mapping atomistic systems to coarse-grained systems

clustering

Cluster analysis tool for heterogenous lipid membranes.

d2l-en

Interactive deep learning book with multi-framework code, math, and discussions. Adopted at 500 universities from 70 countries including Stanford, MIT, Harvard, and Cambridge.

ele

A lightweight package with the periodic table of the elements

eos-ff

To organize CER EOS forcefield development.

example-assignment

An example assignment

example-notebooks

Example Analytic Notebooks Created for BigData and SmartCities Class

fast_wrap

A fast script to wrap atoms or molecules into a simulation box using MDTraj as a backend.

forcefield-utilities

MISC Utilities for MoSDeF Forcefields conversion

forcefield_perfluoroethers

foyer

A package for atom-typing as well as applying and disseminating forcefields

gaff-foyer

glotzerlab-software

Docker image for Glotzer Lab software

gmso

Flexible storage of chemical topology for molecular simulation

gmso-examples

Demonstrating GMSO as a backend for preparing molecular simulation

hoomd-blue

Molecular dynamics and Monte Carlo soft matter simulation on GPUs.

kaggle_novozymes

lammps

Public development project of the LAMMPS MD software package

lipids

My CG lipids

mbuild

A hierarchical, component based molecule builder

mbuild_bilayer

Bilayer builder recipe for mBuild.

mccabegroup

McCabe lab repository for ceramide and phospholipid systems

mdtraj

A modern, open library for the analysis of molecular dynamics trajectories

mosdef-workflows

mosdef_cassandra

MoSDeF compatible wrapper for Cassandra Monte Carlo code

msibi

A package for managing pair-potential derivation using MultiState Iterative Boltzmann Inversion (MS-IBI)