Alternatives and similar repositories for pmda:

Users that are interested in pmda are comparing it to the libraries listed below

• MDAnalysis / panedr
  Reads Gromacs EDR file to populate a pandas dataframe
  ☆31Updated 4 months ago
• jag1g13 / pycgtool
  Generate coarse-grained molecular dynamics models from atomistic trajectories.
  ☆63Updated 2 years ago
• MDAnalysis / WorkshopPrace2021
  Materials for the 2021 PRACE Workshop @ SurfSARA
  ☆31Updated 3 years ago
• bio-phys / PyDHAMed
  Dynamic Histogram Analysis To Determine Free Energies and Rates from Biased Simulations
  ☆20Updated 7 years ago
• MDAnalysis / solvation-analysis
  A comprehensive tool for analyzing liquid solvation structure.
  ☆46Updated 8 months ago
• choderalab / torsionfit
  Bayesian tools for fitting molecular mechanics torsion parameters to quantum chemical data.
  ☆20Updated 3 years ago
• MDAnalysis / MDAPackmol
  MDAnalysis wrapper around Packmol
  ☆30Updated last year
• aa840 / ModSeminario_Py
  Python version of the modified Seminario method code
  ☆16Updated 4 years ago
• shirtsgroup / physical_validation
  Physical validation of molecular simulations
  ☆56Updated 2 months ago
• weiHelloWorld / accelerated_sampling_with_autoencoder
  Accelerated sampling framework with autoencoder-based method
  ☆23Updated 5 years ago
• leelasd / OPLS-AAM
  Implementing OPLS-AA/M Force field in OpenMM from CHARMM formatted parameter files
  ☆12Updated 9 years ago
• lpwgroup / torsiondrive
  Dihedral scanner with wavefront propagation
  ☆33Updated 11 months ago
• dmzuckerman / Sampling-Uncertainty
  Best Practices article intended for LiveCoMS
  ☆39Updated 5 years ago
• leelasd / OPLSAA-DB
  Database of hand-built OPLS-AA parameters and topologies for 464 molecules. Zip files contains parameter and topologies for OpenMM, Groma…
  ☆33Updated 6 years ago
• MDAnalysis / WorkshopHackathon2018
  Materials, issues and things for the 2018 Workshop and Hackathon
  ☆14Updated 5 years ago
• MobleyLab / GuthrieSolv
  Experimental small molecule hydration free energy dataset
  ☆30Updated 2 years ago
• lab-cosmo / sketchmap
  Suite of programs to perform non-linear dimensionality reduction -- sketch-map in particular
  ☆46Updated 5 months ago
• selimsami / qforce
  ☆58Updated 4 months ago
• GilsonLabUCSD / pAPRika
  Advanced toolkit for binding free energy calculations
  ☆32Updated 2 months ago
• FATSLiM / fatslim
  Main code repository for FATSLiM
  ☆21Updated 3 years ago
• MDAnalysis / pytng
  Python bindings for TNG file format
  ☆13Updated 4 months ago
• callumjd / AMBER-Umbrella_COM_restraint_tutorial
  Tutorial to run AMBER umbrella COM restraint code and derive free energy of transfer profile for methanol through DMPC membrane
  ☆30Updated last year
• aspuru-guzik-group / xtb-gaussian
  A wrapper to run xtb inside Gaussian.
  ☆20Updated 4 years ago
• spiwokv / metadynminer
  Package for reading, analysis and visualization of metadynamics HILLS
  ☆34Updated last year
• tbereau / auto_martini
  Automatic MARTINI parametrization of small organic molecules
  ☆66Updated 4 months ago
• openforcefield / openff-evaluator
  A physical property evaluation toolkit from the Open Forcefield Consortium.
  ☆56Updated this week
• OpenFreeEnergy / cinnabar
  Package for consistent reporting of relative free energy results
  ☆38Updated 2 months ago
• harmsm / md-analysis-tools
  scripts for analyzing molecular dynamics trajectories using VMD
  ☆38Updated 9 years ago
• markovmodel / pyemma_tutorials
  How to analyze molecular dynamics data with PyEMMA
  ☆74Updated 5 years ago
• jhenin / Methods-for-enhanced-sampling-and-free-energy-calculations
  Enhanced sampling methods for molecular dynamics simulations
  ☆36Updated 2 years ago