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adkgromacstutorial

Basic tutorial for running and analyzing a Gromacs MD simulation of AdK

alchemical_conformational_analysis

bash_workshop

basicrta

beckernels

A repository of radical.ensemblemd kernels used by the Beckstein Lab

bornprofiler

A small Python package to set up electrostatic solvation free energy ("Born energy") calculations of an ion in a membrane protein and calculate the electrostatic free energy with APBS .

computationalphysics_phy494

Materials for PHY 494

conda-gromacs-2016

Conda package of gromacs 2016 intended for testing purposes.

conda-gromacs-4.6.7

Conda package of gromacs 4.6.7 intended for testing purposes.

conda-gromacs-5.1.2

Conda package of gromacs 5.1.2 intended for testing purposes.

cphmd-analysis

Jack Henderson's CpHMD analysis scripts

gmx_first_aid

A command line utility intended to assist in recovering data from corrupted gromacs trajectories.

gromacswrapper

GromacsWrapper wraps system calls to GROMACS tools into thin Python classes (GROMACS 4.6.5 - 2023 supported).

gromacswrapper.analysis

Legacy code from GromacsWrapper: gromacs.analysis module

h5md_examples

hollow

Fork of Bosco Ho's and Franz Gruswitz's HOLLOW 1.1 (see http://hollow.sourceforge.net/).

hop

Solvent network analysis. Hop is a python package based on MDAnalysis to analyze solvation dynamics.

kda

Python package used for the analysis of biochemical kinetic diagrams.

kda-examples

Kinetic Diagram Analysis Examples

lipidbook

Lipidbook force field repository (public issue tracker and wiki).

making-prettier-plots

a quick primer on making prettier (and more impactful) plots

mdanalysis-with-dask

Benchmarking MDAnalysis with dask.

mdanalysis-workshop

MDAnalysis Tutorial at the 2015 CECAM Macromolecular simulation software workshop

mdpow

Calculation of water/solvent partition coefficients with Gromacs.

mdpow-molconfgen

torsional sampler

mdworks

molecular dynamics, with Fireworks!

minlatex

A minimal working example for an article written in LaTeX

multibind

A Python package for building thermodynamically consistent state graphs.

multibind-publication-code

Repository for the code used in the multibind paper