Alternatives and similar repositories for pytraj

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

• jensengroup / propka
  PROPKA predicts the pKa values of ionizable groups in proteins and protein-ligand complexes based in the 3D structure.
  ☆316Updated last year
• choderalab / yank
  An open, extensible Python framework for GPU-accelerated alchemical free energy calculations.
  ☆187Updated 2 years ago
• Becksteinlab / GromacsWrapper
  GromacsWrapper wraps system calls to GROMACS tools into thin Python classes (GROMACS 4.6.5 - 2024 supported).
  ☆179Updated 2 weeks ago
• Amber-MD / cpptraj
  Biomolecular simulation trajectory/data analysis.
  ☆154Updated this week
• openforcefield / openff-toolkit
  The Open Forcefield Toolkit provides implementations of the SMIRNOFF format, parameterization engine, and other tools. Documentation avai…
  ☆358Updated last week
• Acellera / htmd
  HTMD: Programming Environment for Molecular Discovery
  ☆268Updated 2 months ago
• alanwilter / acpype
  OFFICIAL: AnteChamber PYthon Parser interfacE
  ☆235Updated 3 months ago
• OpenSourceMolecularModeling / OpenSourceMolecularModeling.github.io
  Catalog of Open Source Molecular Modeling Projects
  ☆106Updated 7 months ago
• choderalab / pymbar
  Python implementation of the multistate Bennett acceptance ratio (MBAR)
  ☆269Updated last month
• GrossfieldLab / loos
  LOOS: a lightweight object-oriented structure analysis library
  ☆125Updated 5 months ago
• jalemkul / gmx_tutorials_livecoms
  LiveCoMS GROMACS Tutorials Paper
  ☆126Updated 6 years ago
• westpa / westpa
  WESTPA: The Weighted Ensemble Simulation Toolkit with Parallelization and Analysis
  ☆203Updated last week
• avirshup / py3dmol
  ☆127Updated 9 years ago
• MobleyLab / basic_simulation_training
  A document for the Living Journal of Computational Molecular Science (LiveCoMS) which describes basic training for molecular simulations …
  ☆115Updated 6 years ago
• michellab / Sire
  Sire Molecular Simulations Framework
  ☆96Updated 2 years ago
• MobleyLab / alchemical-analysis
  An open tool implementing some recommended practices for analyzing alchemical free energy calculations
  ☆129Updated last year
• alchemistry / alchemlyb
  the simple alchemistry library
  ☆219Updated 2 weeks ago
• choderalab / openmmtools
  A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine.
  ☆290Updated last week
• openmm / openmmforcefields
  CHARMM and AMBER forcefields for OpenMM (with small molecule support)
  ☆318Updated last week
• marrink-lab / vermouth-martinize
  Describe and apply transformation on molecular structures and topologies
  ☆119Updated last week
• tubiana / TTClust
  clusterize molecular dynamic trajectories (amber, gromacs, charmm, namd, pdb...)
  ☆117Updated last year
• cinfony / cinfony
  Simplified and standard interface to a number of cheminformatics toolkits
  ☆88Updated last year
• deGrootLab / pmx
  Toolkit for free-energy calculation setup/analysis and biomolecular structure handling
  ☆157Updated last month
• project-gemmi / gemmi
  macromolecular crystallography library and utilities
  ☆283Updated 2 weeks ago
• Acellera / moleculekit
  MoleculeKit: Your favorite molecule manipulation kit
  ☆227Updated 2 weeks ago
• Electrostatics / pdb2pqr
  PDB2PQR - determining titration states, adding missing atoms, and assigning charges/radii to biomolecules.
  ☆152Updated 6 months ago
• mittinatten / freesasa
  C-library for calculating Solvent Accessible Surface Areas
  ☆154Updated 2 months ago
• Colvars / colvars
  Collective variables library for molecular simulation and analysis programs
  ☆231Updated last week
• Eigenstate / vmd-python
  Installable VMD as a python module
  ☆146Updated 3 months ago
• choderalab / perses
  Experiments with expanded ensembles to explore chemical space
  ☆192Updated 7 months ago