Repositories list

• kinoml-techpaper-LiveCoMS

  Public
  Fork for safe assurances

  TeX

  •

  Creative Commons Attribution 4.0 International

  •1•0•0•0•Updated Nov 20, 2025Nov 20, 2025

• review-protein-benchmark-datasets

  Public
  TeX

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  Creative Commons Attribution 4.0 International

  •1•0•0•0•Updated Oct 27, 2025Oct 27, 2025

• westpa_tutorials

  Public
  Tutorials and additional documentation for the WESTPA suite

  Jupyter Notebook

  •22•1•0•0•Updated Oct 20, 2025Oct 20, 2025

• BPIPMDS

  Public
  Best Practices for Computing Interfacial Properties from Molecular Dynamics Simulations

  TeX

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  Creative Commons Attribution 4.0 International

  •4•0•0•0•Updated Oct 17, 2025Oct 17, 2025

• software-physical-validation

  Public
  Best Practices article (intended for LiveCoMS) treating simulation software validation and physical validation

  BibTeX Style

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  Other

  •2•0•0•0•Updated Oct 17, 2025Oct 17, 2025

• Sampling-Uncertainty

  Public
  Best Practices article intended for LiveCoMS

  TeX

  •5•2•0•0•Updated Oct 17, 2025Oct 17, 2025

• tinker-hp

  Public
  Tinker-HP: High-Performance Massively Parallel Evolution of Tinker on CPUs & GPUs

  C

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  Other

  •28•0•0•0•Updated Oct 17, 2025Oct 17, 2025

• protein-ligand-benchmark-livecoms

  Public
  Jupyter Notebook

  •3•0•0•0•Updated Oct 17, 2025Oct 17, 2025

• CpHMD-Tutorial

  Public
  Github repository for the LiveCoMS tutorial of the continuous constant pH molecular dynamics method

  TeX

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  Creative Commons Attribution 4.0 International

  •2•0•0•0•Updated Oct 17, 2025Oct 17, 2025

• gromos_tutorial_livecoms

  Public
  TeX

  •8•0•0•0•Updated Oct 17, 2025Oct 17, 2025

• dmol-book

  Public
  Deep learning for molecules and materials book

  Jupyter Notebook

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  Other

  •129•0•0•0•Updated Oct 13, 2025Oct 13, 2025

• biosimspace_tutorials

  Public
  A tutorials suite for BioSimSpace.

  Jupyter Notebook

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  GNU General Public License v3.0

  •7•0•0•0•Updated Oct 10, 2025Oct 10, 2025

• lammpstutorials-article

  Public
  A Set of Tutorials for the LAMMPS Simulation Package

  Jupyter Notebook

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  Creative Commons Attribution 4.0 International

  •3•0•0•0•Updated Oct 1, 2025Oct 1, 2025

• MD_FromBasicsToApplication

  Public
  Elaborate Tutorial for Teaching Molecular Dynamics directed to university students in their graduate program. The course is designed to be finished within one semester, but can be completed within a couple of weeks technically speaking.

  Jupyter Notebook

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  MIT License

  •12•0•0•0•Updated Sep 11, 2025Sep 11, 2025

• best-practices-mc

  Public
  TeX

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  Other

  •3•0•0•0•Updated Aug 21, 2025Aug 21, 2025

• gist-tutorial

  Public
  GIST Tutorial published in the Living Journal of Computational Molecular Science

  TeX

  •2•0•0•0•Updated Aug 14, 2025Aug 14, 2025

• gamd_livecoms_tutorial

  Public
  TeX

  •1•0•0•0•Updated Jul 8, 2025Jul 8, 2025

• SAFEP_tutorial

  Public
  A tutorial for Streamlined Alchemical Free Energy Perturbations with NAMD

  TeX

  •4•0•0•0•Updated Mar 20, 2025Mar 20, 2025

• SEEKR_tutorials

  Public
  An Introductory Tutorial to the SEEKR2 (Simulation Enabled Estimation of Kinetic Rates v. 2) Multiscale Milestoning Software

  M4

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  BSD 3-Clause "New" or "Revised" License

  •1•0•0•0•Updated Jul 28, 2024Jul 28, 2024

• livecomsjournal.github.io

  Public
  Content for policy/instructional pages of the Living Journal of Computational Molecular Science (LiveCoMS)

  sciencejournalmolecular-dynamics+ 4computational-biologypublishingcomputational-chemistrymolecular-modeling

  SCSS

  •15•6•19•3•Updated Oct 23, 2023Oct 23, 2023

• Methods-for-enhanced-sampling-and-free-energy-calculations

  Public
  Enhanced sampling methods for molecular dynamics simulations

  TeX

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  Creative Commons Attribution 4.0 International

  •4•0•0•0•Updated Dec 16, 2022Dec 16, 2022

• pysimm_lcms_guide

  Public
  Jupyter Notebook

  •1•0•0•0•Updated Nov 8, 2022Nov 8, 2022

• article_templates

  Public
  Templates for use in preparing articles for the Living Journal of Computational Molecular Sciences (LiveCoMS)

  sciencejournalpublishing+ 2latex-templatescientific-publications

  TeX

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  Creative Commons Attribution 4.0 International

  •15•10•15•3•Updated Sep 19, 2022Sep 19, 2022

• livecoms-atomistic-software

  Public
  Git repository accompanying the LiveCoMS perpetual review on atomistic.software

  TeX

  •1•0•0•0•Updated Aug 30, 2022Aug 30, 2022

• hdxer_tutorials_livecoms

  Public
  Repository for the LiveCoMS HDXer tutorials article

  TeX

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  Other

  •1•0•0•0•Updated Aug 30, 2022Aug 30, 2022

• software-community

  Public
  Alan Grossfield LiveCoMS article

  TeX

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  Creative Commons Attribution 4.0 International

  •15•0•0•0•Updated Aug 24, 2022Aug 24, 2022

• kinase_similarity_pipeline_paper

  Public
  Kinase Similarity Assessment Pipeline For Off-Target Prediction

  TeX

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  Creative Commons Attribution 4.0 International

  •1•0•0•0•Updated Jun 23, 2022Jun 23, 2022

• alchemical-best-practices

  Public
  Best practice document for alchemical free energy calculations going to livecoms journal

  Jupyter Notebook

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  Creative Commons Attribution 4.0 International

  •26•1•0•0•Updated Mar 17, 2021Mar 17, 2021

• aqua-duct_tutorials_livecoms

  Public
  This document presents six tutorials which explain all available functionalities in AQUA-DUCT, a software package for analysis of molecular dynamics (MD) simulations.

  TeX

  •1•0•0•0•Updated Mar 8, 2021Mar 8, 2021

• journal_information

  Public
  Information and documents supporting the work of the Living Journal of Computational Molecular Sciences (LiveCoMS)

  sciencepublishingpreprints+ 3journalsscience-researchscience-journal

  TeX

  •4•8•13•0•Updated Oct 12, 2020Oct 12, 2020