bio-phys

MDBenchmark

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

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.

cadishi

Cadishi: CAlculation of DIStance HIstograms

BioEn

BioEn - Bayesian Inference Of ENsembles

cnt-martini

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

DiffusionGLS

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

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.

aimmd

capriqorn

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

memdiff

Implementation of corrections for diffusion coefficients in membrane simulations.

asyncmd

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

complexespp

Coarse-grained simulations of biomolecular complexes

hierarchical-chain-growth

Grow ensembles of disordered biomolecules from fragment libraries

trimem

Monte Carlo sampling of the Helfrich bending energy.

Magnesium-FFs

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

constraint-coupling-analysis

DiffusionMLE

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

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.

optimizedMgFFs

Optimized force field parameters for Magnesium in combination with the SPC/E, TIP3P-fb, TIP4P/2005, TIP4P-Ew, or TIP4P-D water model for all-atom MD simulations.

SAXS_BioEn

BioFF

Bayesian inference of force fields

ForceFieldsMC3

hplusminus

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

MgFF_OPC

Magnesium Force Fields for OPC Water with Accurate Solvation, Ion-Binding, and Water-Exchange Properties: Successful Transfer from SPC/E

RebindingKineticsMLE

Analyze pulling traces from single-molecule force spectroscopy experiments close to equilibrium to extract on and off rates and parameters characterizing the free-energy profile underlying the bond.

BioEn.jl

BioEn optimization

cnt-clusters

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

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)

RefinementModels.jl

VantHoffFitting

Nonlinear least squares fitting of van 't Hoff plots via cubic splines, which makes the extraction of heat capacity and thermodynamic potentials possible.