Alternatives and similar repositories for MDanalysis_Workshop

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

• MobleyLab / SeparatedTopologies
  Exploratory work on free energy calculations with GROMACS using "separated topologies" approach (Rocklin et al., 2013).
  ☆28Updated last year
• openmm / openmm_workshops
  ☆42Updated last year
• rinikerlab / restraintmaker
  Restraintmaker is a tool intended to build Position or Distance restraints for Molecular Dynamics simulations (or any other simulation te…
  ☆19Updated 3 years ago
• mobiochem / MoBioTools
  A simple yet versatile toolkit to setup quantum mechanical/molecular mechanical (QM/MM) calculations from molecular dynamics trajectories…
  ☆30Updated 2 years ago
• bioexcel / cp2K_qmmm_tutorials_for_biological_simulations
  Several QM/MM tutorials for biological simulations adapted to CP2K. Tutorials adapted from AMBER, GMX, NAMD and CPMD softwares.
  ☆24Updated 6 years ago
• choderalab / espaloma-charge
  Standalone charge assignment from Espaloma framework.
  ☆46Updated 3 months ago
• MDAnalysis / UserGuide
  User Guide for MDAnalysis
  ☆29Updated last week
• openforcefield / openff-sage
  Scripts, inputs and the results generated as part of the training the Sage line of OpenFF force fields.
  ☆21Updated 7 months ago
• qusers / Q6
  Q6 Repository -- EVB, FEP and LIE simulator.
  ☆35Updated 2 years ago
• OpenFreeEnergy / feflow
  Recipes and protocols for molecular free energy calculations using the openmmtools/perses and Open Free Energy toolkits
  ☆15Updated 2 weeks ago
• OpenBioSim / biosimspace_tutorials
  A tutorials suite for BioSimSpace.
  ☆34Updated 3 months ago
• choderalab / pymbar-examples
  Examples of applications of pymbar to various problems in simulation and experiment
  ☆23Updated 11 years ago
• choderalab / kinase-metadynamics
  To run metadynamics simulations using openMM (based on Peter Eastman's script)
  ☆13Updated 6 years ago
• samplchallenges / SAMPL9
  ☆31Updated 2 years ago
• insilichem / ommprotocol
  A command line application to launch molecular dynamics simulations with OpenMM
  ☆40Updated 3 years ago
• SimonBoothroyd / absolv
  Absolute solvation free energy calculations with OpenFF and OpenMM
  ☆26Updated last year
• openforcefield / ccpbiosim-2023
  Materials for 2023 workshop at CCPBioSim Training Week https://www.ccpbiosim.ac.uk/events/upcoming-events/eventdetail/104/-/training-week
  ☆31Updated 2 years ago
• SimonBoothroyd / plotmol
  Interactive plotting of data annotated with molecule structures.
  ☆12Updated 2 years ago
• RedesignScience / cvpack
  Useful Collective Variables for OpenMM
  ☆17Updated last year
• Abdelazim-Abdelgawwad / easyPARM
  easyPARM is a computational tool developed to simplify the derivation of force field parameters for metal-containing molecular systems an…
  ☆31Updated last week
• OpenFreeEnergy / ExampleNotebooks
  Notebooks demonstrating how to do simple tasks related to free energy calculations.
  ☆58Updated this week
• gpantel / MD_methods-and-analysis
  Repository for MD methods and analysis from submitted or published work
  ☆20Updated 2 years ago
• OpenFreeEnergy / cinnabar
  Package for consistent reporting of relative free energy results
  ☆41Updated last week
• openforcefield / smirnoff-plugins
  Plugins to enable using custom functional forms in SMIRNOFF based force fields
  ☆11Updated 2 weeks ago
• GoMartini3-tools / Native-contacts-determination-from-MD
  We provide a set of scripts to calculate native contacts from a MD. Native contacts are determined according to the overlap and rCSU appr…
  ☆16Updated last year
• PodewitzLab / PyConSolv
  ☆27Updated 6 months ago
• drazen-petrov / SMArt
  ☆31Updated this week
• vuqv / cosmo
  COSMO: COarse-grained Simulation of intrinsically disordered prOteins with openMM
  ☆15Updated 5 months ago
• MDAnalysis / WorkshopMDMLEdinburgh2022
  ☆65Updated 6 months ago
• dspoel / remd-temperature-generator
  Temperature generator for Replica Exchange MD simulations
  ☆30Updated 3 years ago