Pinned Repositories
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.
BioEn
BioEn - Bayesian Inference Of ENsembles
cadishi
Cadishi: CAlculation of DIStance HIstograms
capriqorn
Capriqorn: CAlculation of P(R) and I(Q) Of macRomolecules in solutioN
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-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.
MDBenchmark
Quickly generate, start and analyze benchmarks for molecular dynamics simulations.
PyDHAMed
Dynamic Histogram Analysis To Determine Free Energies and Rates from Biased Simulations
pydiffusion
Analyse Rotational Diffusion Tensor from MD Simulations
bio-phys's Repositories
bio-phys/MDBenchmark
Quickly generate, start and analyze benchmarks for molecular dynamics simulations.
bio-phys/BioEn
BioEn - Bayesian Inference Of ENsembles
bio-phys/pydiffusion
Analyse Rotational Diffusion Tensor from MD Simulations
bio-phys/cnt-martini
Generates Martini models for open carbon nanotubes to use with Gromacs.
bio-phys/DiffusionGLS
Estimate the self-diffusion coefficient of a trajectory with a Generalized Least Squares (GLS) optimization procedure.
bio-phys/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.
bio-phys/aimmd
bio-phys/capriqorn
Capriqorn: CAlculation of P(R) and I(Q) Of macRomolecules in solutioN
bio-phys/memdiff
Implementation of corrections for diffusion coefficients in membrane simulations.
bio-phys/asyncmd
asyncmd is a library to write concurrent code for setup, run and analysis of molecular dynamics simulations using pythons async/await synthax.
bio-phys/complexespp
Coarse-grained simulations of biomolecular complexes
bio-phys/hierarchical-chain-growth
Grow ensembles of disordered biomolecules from fragment libraries
bio-phys/trimem
Monte Carlo sampling of the Helfrich bending energy.
bio-phys/Magnesium-FFs
Optimized force field parameters for Magnesium in combination with the TIP3P water model for all-atom MD simulations.
bio-phys/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.
bio-phys/constraint-coupling-analysis
bio-phys/DiffusionMLE
Analyze experimental tracking data using a maximum likelihood estimator (MLE) to extract translational diffusion coefficients.
bio-phys/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.
bio-phys/SAXS_BioEn
bio-phys/af2_lir_screen
bio-phys/BioFF
Bayesian inference of force fields
bio-phys/ForceFieldsMC3
bio-phys/hplusminus
Statistical tests to detect and quantify correlations in residuals when fitting models to one-dimensional data.
bio-phys/MgFF_OPC
Magnesium Force Fields for OPC Water with Accurate Solvation, Ion-Binding, and Water-Exchange Properties: Successful Transfer from SPC/E
bio-phys/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.
bio-phys/VantHoffFitting
Nonlinear least squares fitting of van 't Hoff plots via cubic splines, which makes the extraction of heat capacity and thermodynamic potentials possible.
bio-phys/BioEn.jl
BioEn optimization
bio-phys/cnt-clusters
Simulation parameters and results for lipid-mediated self-assembly of CNT membranes.
bio-phys/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)
bio-phys/RefinementModels.jl