MobleyLab / alchemical-analysis

Related projects ⓘ

Alternatives and complementary repositories for alchemical-analysis

• alchemistry / alchemlyb
  the simple alchemistry library
  ☆197Updated last week
• ricalessandri / Martini3-small-molecules
  Martini 3 small-molecule database
  ☆54Updated 2 months ago
• openpathsampling / openpathsampling
  An open source Python framework for transition interface and path sampling calculations.
  ☆105Updated 3 weeks ago
• marrink-lab / vermouth-martinize
  Describe and apply transformation on molecular structures and topologies
  ☆97Updated this week
• MobleyLab / FreeSolv
  Experimental and calculated small molecule hydration free energies
  ☆104Updated 2 years ago
• MCompChem / fep-benchmark
  Benchmark set for relative free energy calculations.
  ☆97Updated 5 months ago
• marrink-lab / polyply_1.0
  Generate input parameters and coordinates for atomistic and coarse-grained simulations of polymers, ssDNA, and carbohydrates
  ☆127Updated 3 weeks ago
• deGrootLab / pmx
  Toolkit for free-energy calculation setup/analysis and biomolecular structure handling
  ☆134Updated 2 months ago
• patonlab / GoodVibes
  Calculate quasi-harmonic free energies from Gaussian output files with temperature and other corrections
  ☆136Updated 2 months ago
• shirtsgroup / InterMol
  Conversion tool for molecular simulations
  ☆188Updated 4 months ago
• Isra3l / ligpargen
  ☆59Updated 3 weeks ago
• Marcello-Sega / pytim
  a python package for the interfacial analysis of molecular simulations
  ☆80Updated this week
• MobleyLab / basic_simulation_training
  A document for the Living Journal of Computational Molecular Science (LiveCoMS) which describes basic training for molecular simulations …
  ☆109Updated 5 years ago
• tbereau / auto_martini
  Automatic MARTINI parametrization of small organic molecules
  ☆61Updated this week
• Becksteinlab / GromacsWrapper
  GromacsWrapper wraps system calls to GROMACS tools into thin Python classes (GROMACS 4.6.5 - 2024 supported).
  ☆169Updated last month
• NNairIITK / Enhanced_Sampling_Methods_Tutorials
  Tutorials of few enhanced sampling methods along with bash script to run the method in a single shot..
  ☆41Updated 3 years ago
• cole-group / FEgrow
  An Open-Source Molecular Builder and Free Energy Preparation Workflow
  ☆118Updated 3 weeks ago
• tubiana / TTClust
  clusterize molecular dynamic trajectories (amber, gromacs, charmm, namd, pdb...)
  ☆107Updated 6 months ago
• choderalab / yank
  An open, extensible Python framework for GPU-accelerated alchemical free energy calculations.
  ☆181Updated last year
• openmm / openmm-plumed
  OpenMM plugin to interface with PLUMED
  ☆59Updated 6 months ago
• maccallumlab / martini_openmm
  ☆49Updated last year
• openforcefield / openff-forcefields
  Force fields produced by the Open Force Field Initiative
  ☆140Updated this week
• qubekit / QUBEKit
  Quantum Mechanical Bespoke Force Field Derivation Toolkit
  ☆95Updated 4 months ago
• luancarvalhomartins / PyAutoFEP
  PyAutoFEP: an automated FEP workflow for GROMACS integrating enhanced sampling methods
  ☆162Updated last year
• fhh2626 / BFEE2
  binding free energy estimator 2
  ☆105Updated this week
• jvalegre / aqme
  Automated Quantum Mechanical Environments (AQME) offers transparent and reproducible workflows available for Jupyter Notebooks and comman…
  ☆98Updated this week
• Tsjerk / Insane
  INSert membrANE - A simple, versatile tool for building coarse-grained simulation systems
  ☆45Updated 6 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
• paulrobustelli / CHEM101.6
  ☆123Updated 7 months ago
• digital-chemistry-laboratory / morfeus
  A Python package for calculating molecular features
  ☆164Updated 9 months ago