nkm-ml Goto Github PK

martinize.py

Create coarse grain Martini input files for Gromacs from (atomistic) pdb files.

match

mbuild-examples

mBuild examples

md-task

Tool suite for analysing molecular dynamics trajectories using network analysis and PRS

mdanalysiscookbook

Examples and tutorials of using MDAnalysis

mdanalysistutorial

Tutorial for MDAnalysis.

mdp-machine-learning

MDP Machine Learning Lecture

mdtraj

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

memsurfer

MemSurfer is a software tool to compute bilayer membrane surfaces.

memtools

A python package for the extraction of memory kernels from time series

ml_mdps

mldl-md-dynamics

A repository of update in molecular dynamics field by recent progress in machine learning and deep learning.

mmgbsa

Some code to extract data from Amber 15 MMGBSA.py output

moleculargnn_smiles

The code of a graph neural network (GNN) for molecules, which is based on learning representations of r-radius subgraphs (i.e., fingerprints) in molecules.

mosdef-workflows

Sample molecular simulation workflows using a MoSDeF and community tools

multilayergm-matlab

A generative model for mesoscale structure in multilayer networks implemented in MATLAB

n2p2

n2p2 - A Neural Network Potential Package

networkanalysis

Java package that provides data structures and algorithms for network analysis.

networkx

Network Analysis in Python

networkx-notebook

Jupyter notebook for NetworkX exploration.

nglview

Jupyter widget to interactively view molecular structures and trajectories

nmea-paper

Scripts used to generate data and figures for anisotropic terahertz spectroscopy paper

nmoldyn3

Analysis of Molecular Dynamics trajectories

notebook_tutorials

A home for the Jupyter notebook tutorials created by and for our lab

notebooks

Repository that contains my research

notebooks-1

Examples and IPython Notebooks about NetworkX

notebooks-statistics-and-machinelearning

Jupyter Notebooks from the old UnsupervisedLearning.com (RIP) machine learning and statistics blog

openmm-tutorial-msbs

OpenMM tutorial for the MSBS course

order

:potable_water: A tool to characterize the local structure of liquid water by geometric order parameters.

packmem

packmem: a tool to compute interfacial packing defects in simulated membranes