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aimmd

asyncmd

asyncmd is a library to write concurrent code for setup, run and analysis of molecular dynamics simulations using pythons async/await synthax.

binless-wham

Binless weighted histogram analysis

bioem

GPU accelerating computing for Bayesian inference of electron microscopy images. BioEM is a publicly available software that enables the characterization of structural models with respect to individual electron microscopy images.

bioem-tutorials

Tutorials for BioEM

bioen

BioEn - Bayesian Inference Of ENsembles

bioen.jl

BioEn optimization

bioff

Bayesian inference of force fields

cadishi

Cadishi: CAlculation of DIStance HIstograms

capriqorn

Capriqorn: CAlculation of P(R) and I(Q) Of macRomolecules in solutioN

cnt-clusters

Simulation parameters and results for lipid-mediated self-assembly of CNT membranes.

cnt-gaff

Build atomistic structures of carbon nanotubes with the possibility to add functional groups (OH, COOH, COO-) and assigns generalized Amber (GAFF) parameters to them.

cnt-lipid14-analysis

Analysis tools for simulations of carbon nanotubes (CNTs) in lipid membranes modeled with the Lipid14 force field.

cnt-martini

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

cnt-martini-analysis

Analysis tools for Martini simulations of a single carbon nanotube porin in a lipid membrane. Mostly also work for membrane proteins.

complexespp

Coarse-grained simulations of biomolecular complexes

constraint-coupling-analysis

diffusiongls

Estimate the self-diffusion coefficient of a trajectory with a Generalized Least Squares (GLS) optimization procedure.

diffusionmle

Analyze experimental tracking data using a maximum likelihood estimator (MLE) to extract translational diffusion coefficients.

ff-mg-ca-nucleicacids

Extension for the interactions with DNA and RNA of our previously bulk-optimized force field parameters (https://doi.org/10.1063/1.5017694)

force-fields-for-metal-cations

Optimized force field parameters for metal cations (Li+, Na+, K+, Cs+, Mg2+, Ca2+, Sr2+, and Ba2+) in combination with the TIP3P water model for all-atom MD simulations.

forcefieldsmc3

forcespectroscopymle

Analyze rupture force spectra from single-molecule force spectroscopy experiments to extract disassociation rates and parameters characterizing the free-energy profile underlying the bond.

hierarchical-chain-growth

Grow ensembles of disordered biomolecules from fragment libraries

hplusminus

Statistical tests to detect and quantify correlations in residuals when fitting models to one-dimensional data.

kinetics-remd

Extracting kinetics from replica exchange molecular dynamics and related methods that produce discontinuous trajectories.

magnesium-ffs

Optimized force field parameters for Magnesium in combination with the TIP3P water model for all-atom MD simulations.

mdbenchmark

Quickly generate, start and analyze benchmarks for molecular dynamics simulations.

memcurv

Software to characterize membrane shape and curvature

memdiff

Implementation of corrections for diffusion coefficients in membrane simulations.