Alternatives and similar repositories for PyDHAMed

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

• jag1g13 / pycgtool
  Generate coarse-grained molecular dynamics models from atomistic trajectories.
  ☆64Updated last month
• BrooksResearchGroup-UM / FastMBAR
  A fast solver for large scale MBAR/UWHAM equations
  ☆40Updated last year
• MobleyLab / benchmarksets
  Benchmark sets for binding free energy calculations: Perpetual review paper, discussion, datasets, and standards
  ☆46Updated 4 years ago
• FATSLiM / fatslim
  Main code repository for FATSLiM
  ☆23Updated 3 years ago
• MDAnalysis / panedr
  Reads Gromacs EDR file to populate a pandas dataframe
  ☆33Updated 2 months ago
• tbereau / auto_martini
  Automatic MARTINI parametrization of small organic molecules
  ☆71Updated 6 months ago
• shirtsgroup / physical_validation
  Physical validation of molecular simulations
  ☆57Updated 2 months ago
• choderalab / torsionfit
  Bayesian tools for fitting molecular mechanics torsion parameters to quantum chemical data.
  ☆21Updated 4 years ago
• openmm / openmm-plumed
  OpenMM plugin to interface with PLUMED
  ☆72Updated last month
• Becksteinlab / MDPOW
  Calculation of water/solvent partition coefficients with Gromacs.
  ☆28Updated last year
• openforcefield / smirnoff99Frosst
  A general small molecule force field descended from AMBER99 and parm@Frosst, available in the SMIRNOFF format
  ☆31Updated last week
• MobleyLab / blues
  Applications of nonequilibrium candidate Monte Carlo (NCMC) to ligand binding mode sampling
  ☆34Updated last month
• bio-phys / MDBenchmark
  Quickly generate, start and analyze benchmarks for molecular dynamics simulations.
  ☆80Updated last year
• MDAnalysis / pmda
  Parallel algorithms for MDAnalysis
  ☆31Updated last year
• essex-lab / grand
  A Python module for carrying out GCMC insertions and deletions of water molecules in OpenMM.
  ☆72Updated 2 years ago
• openpathsampling / openpathsampling
  An open source Python framework for transition interface and path sampling calculations.
  ☆115Updated last week
• p-j-smith / lipyphilic
  A Python toolkit for the analyis of lipid membrane simulations
  ☆33Updated 2 months ago
• kassonlab / gmxapi
  (outdated) fork of https://gitlab.com/gromacs/gromacs
  ☆53Updated 2 years ago
• jhenin / Methods-for-enhanced-sampling-and-free-energy-calculations
  Enhanced sampling methods for molecular dynamics simulations
  ☆41Updated 3 years ago
• GMPavanLab / Swarm-CG
  Swarm-CG: Automatic Parametrization of Bonded Terms in MARTINI-based Coarse-Grained Models of Simple to Complex Molecules via Fuzzy Self-…
  ☆45Updated last year
• MDAnalysis / membrane-curvature
  MDAnalysis tool to calculate membrane curvature.
  ☆35Updated 5 months ago
• MobleyLab / FreeSolv
  Experimental and calculated small molecule hydration free energies
  ☆128Updated 3 years ago
• RMeli / spyrmsd
  📐 Symmetry-corrected RMSD in Python
  ☆109Updated this week
• lpwgroup / torsiondrive
  Dihedral scanner with wavefront propagation
  ☆36Updated 7 months ago
• tiwarylab / amino
  Automatic Mutual Information Noise Omission
  ☆15Updated last year
• alchemistry / alchemical-best-practices
  Best practice document for alchemical free energy calculations going to livecoms journal
  ☆80Updated last week
• LoLab-MSM / PyBILT
  Toolkit to aid in the analysis of lipid bilayer molecular simulation trajectories.
  ☆26Updated 4 years ago
• lab-cosmo / sketchmap
  Suite of programs to perform non-linear dimensionality reduction -- sketch-map in particular
  ☆47Updated last year
• delemottelab / string-method-swarms-trajectories
  A python implementation of the string method with swarms of trajectories using GROMACS
  ☆18Updated 3 years ago
• tiwarylab / SGOOP
  Spectral Gap Optimization of Parameters
  ☆18Updated 5 years ago