Skip to content

@livecomsjournal Living Journal of Computational Molecular Science

Change the repository type filter

All

    Repositories list

    40 repositories

    • lammpstutorials-article

      Public
      A Set of Tutorials for the LAMMPS Simulation Package
      Jupyter Notebook
      •
      Creative Commons Attribution 4.0 International
      •3•0•0•0•Updated Apr 10, 2026Apr 10, 2026

    • article_templates

      Public
      Templates for use in preparing articles for the Living Journal of Computational Molecular Sciences (LiveCoMS)
      sciencejournalpublishing
      sciencejournalpublishinglatex-templatescientific-publications
      TeX
      •
      Creative Commons Attribution 4.0 International
      •15•10•14•3•Updated Mar 27, 2026Mar 27, 2026

    • SAFEP_tutorial

      Public
      A tutorial for Streamlined Alchemical Free Energy Perturbations with NAMD
      TeX
      •4•0•0•0•Updated Mar 2, 2026Mar 2, 2026

    • dmol-book

      Public
      Deep learning for molecules and materials book
      Jupyter Notebook
      •
      Other
      •135•0•0•0•Updated Feb 21, 2026Feb 21, 2026

    • tinker-hp

      Public
      Tinker-HP: High-Performance Massively Parallel Evolution of Tinker on CPUs & GPUs
      C
      •
      Other
      •28•0•0•0•Updated Jan 26, 2026Jan 26, 2026

    • best-practices-namd

      Public
      Best practices Guide on nonadiabatic molecular dynamics
      TeX
      •1•0•0•0•Updated Jan 22, 2026Jan 22, 2026

    • ModXNALiveComs

      Public
      master repository for modXNA LiveCommons tutorial
      TeX
      •
      Creative Commons Attribution 4.0 International
      •1•0•0•0•Updated Dec 31, 2025Dec 31, 2025

    • livecomsjournal.github.io

      Public
      Content for policy/instructional pages of the Living Journal of Computational Molecular Science (LiveCoMS)
      sciencejournalmolecular-dynamics
      sciencejournalmolecular-dynamicscomputational-biologypublishingcomputational-chemistrymolecular-modeling
      SCSS
      •15•6•19•3•Updated Dec 2, 2025Dec 2, 2025

    • 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
      •
      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
      •
      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
      •
      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

    • 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
      •
      Creative Commons Attribution 4.0 International
      •3•0•0•0•Updated Oct 17, 2025Oct 17, 2025

    • gromos_tutorial_livecoms

      Public
      TeX
      •9•0•0•0•Updated Oct 17, 2025Oct 17, 2025

    • biosimspace_tutorials

      Public
      A tutorials suite for BioSimSpace.
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •8•0•0•0•Updated Oct 10, 2025Oct 10, 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 s…
      Jupyter Notebook
      •
      MIT License
      •12•0•0•0•Updated Sep 11, 2025Sep 11, 2025

    • best-practices-mc

      Public
      TeX
      •
      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
      •3•0•0•0•Updated Aug 14, 2025Aug 14, 2025

    • gamd_livecoms_tutorial

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

    • SEEKR_tutorials

      Public
      An Introductory Tutorial to the SEEKR2 (Simulation Enabled Estimation of Kinetic Rates v. 2) Multiscale Milestoning Software
      M4
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•0•Updated Jul 28, 2024Jul 28, 2024

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

      Public
      Enhanced sampling methods for molecular dynamics simulations
      TeX
      •
      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

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

    • software-community

      Public
      Alan Grossfield LiveCoMS article
      TeX
      •
      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
      •
      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
      •
      Creative Commons Attribution 4.0 International
      •28•1•0•0•Updated Mar 17, 2021Mar 17, 2021
    ProTip! When viewing an organization's repositories, you can use the props. filter to filter by custom property.