markovmodel / PyEMMA_IPython

Related projects ⓘ

Alternatives and complementary repositories for PyEMMA_IPython

• markovmodel / adaptivemd
  A python framework to run adaptive Markov state model (MSM) simulation on HPC resources
  ☆18Updated 7 months ago
• markovmodel / pyemma-workshop
  ☆26Updated 2 years ago
• markovmodel / thermotools
  Winter is coming...
  ☆12Updated 5 years ago
• markovmodel / pytram
  The pytram package is deprecated and no longer supported. We recommend to switch to PyEMMA
  ☆9Updated 8 years ago
• markovmodel / msmtools
  Tools for estimating and analyzing Markov state models
  ☆40Updated 2 years ago
• NREL / alfabet
  Machine learning predictions of bond dissociation energy
  ☆57Updated 2 months ago
• learningmatter-mit / Coarse-Graining-Auto-encoders
  ☆21Updated 5 years ago
• markovmodel / pyemma_tutorials
  How to analyze molecular dynamics data with PyEMMA
  ☆72Updated 5 years ago
• hsidky / srv
  ☆15Updated 4 years ago
• msultan / vde_metadynamics
  Enhanced protein mutational sampling using time-lagged variational autoencoders
  ☆29Updated 6 years ago
• wehs7661 / ensemble_md
  A python package for performing GROMACS simulation ensembles
  ☆13Updated this week
• Becksteinlab / MDPOW
  Calculation of water/solvent partition coefficients with Gromacs.
  ☆25Updated last month
• DingGroup / BayesMBAR
  Bayesian Multistate Bennett Acceptance Ratio Method
  ☆12Updated 3 weeks ago
• noegroup / reform
  A simple implementation of replica exchange MD simulations for OpenMM.
  ☆22Updated 3 years ago
• OpenFreeEnergy / cinnabar
  Package for consistent reporting of relative free energy results
  ☆37Updated 5 months ago
• wehs7661 / enhanced_sampling_tutorials
  A repository providing jupyter notebooks and simulation inputs that accompany the mini course Hands-on tutorials: Advanced sampling metho…
  ☆12Updated last month
• hsidky / ann_sampling
  Learning free energy landscapes using artificial neural networks
  ☆14Updated 6 years ago
• andrrizzi / tfep-revisited-2021
  Source code and input files associated to the paper "Targeted free energy perturbation revisited: Accurate free energies from mapped refe…
  ☆13Updated 3 years ago
• ochsenfeld-lab / adaptive_sampling
  Adaptive sampling algorithms for molecular transitions
  ☆12Updated this week
• Tsjerk / Backward
  Mapping from Coarse Grain Models to Atomistic (and Back)
  ☆15Updated last year
• torchmd / torchmd-cg
  Example to fit parameters and run CG simulations using TorchMD and Schnet
  ☆42Updated 2 years ago
• mms-fcul / PypKa
  A python module for flexible Poisson-Boltzmann based pKa calculations with proton tautomerism
  ☆56Updated 9 months ago
• GOMC-WSU / py-MCMD
  This python code creates hybrid MD/MC (NAMD/GOMC) simulations for the NVT, NPT, GCMC, and GEMC-NVT ensembles
  ☆32Updated last month
• MobleyLab / SolvationToolkit
  In-house tools for setting up arbitrary solute-solvent mixtures for simulation in GROMACS, Amber, OpenMM or other codes
  ☆31Updated 4 years ago
• wwang2 / CoarseGrainingVAE
  Geometric super-resolution for molecular geometries
  ☆38Updated 2 years ago
• seekrcentral / seekr2
  Simulation-Enabled Estimation of Kinetic Rates - Version 2
  ☆27Updated 3 weeks ago
• matteoferla / molecular_rectifier
  Given an RDKit molecule that does not sanitise, correct it until it does
  ☆36Updated 7 months ago
• LQCT / MDScan
  An efficient approach to RMSD-Based HDBSCAN Clustering of long Molecular Dynamics
  ☆15Updated 2 years ago
• choderalab / torsionfit
  Bayesian tools for fitting molecular mechanics torsion parameters to quantum chemical data.
  ☆19Updated 3 years ago
• radakb / pynamd
  Python Tools for NAMD
  ☆19Updated last year