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    21 repositories

    • livecomsjournal.github.io

      Public
      Content for policy/instructional pages of the Living Journal of Computational Molecular Science (LiveCoMS)
      sciencejournalmolecular-dynamicscomputational-biologypublishingcomputational-chemistrymolecular-modeling
      SCSS
      •15•6•19•3•Updated Oct 23, 2023Oct 23, 2023

    • article_templates

      Public
      Templates for use in preparing articles for the Living Journal of Computational Molecular Sciences (LiveCoMS)
      sciencejournalpublishinglatex-templatescientific-publications
      TeX
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      Creative Commons Attribution 4.0 International
      •14•9•15•2•Updated Sep 19, 2022Sep 19, 2022

    • protein-ligand-benchmark-livecoms

      Public
      Jupyter Notebook
      •3•0•0•0•Updated Aug 30, 2022Aug 30, 2022

    • CpHMD-Tutorial

      Public
      Github repository for the LiveCoMS tutorial of the continuous constant pH molecular dynamics method
      TeX
      •
      Creative Commons Attribution 4.0 International
      •2•0•0•0•Updated Aug 18, 2022Aug 18, 2022

    • gromos_tutorial_livecoms

      Public
      TeX
      •7•0•0•0•Updated Mar 18, 2021Mar 18, 2021

    • alchemical-best-practices

      Public
      Best practice document for alchemical free energy calculations going to livecoms journal
      Jupyter Notebook
      •
      Creative Commons Attribution 4.0 International
      •18•1•0•0•Updated Mar 17, 2021Mar 17, 2021

    • BPIPMDS

      Public
      Best Practices for Computing Interfacial Properties from Molecular Dynamics Simulations
      TeX
      •
      Creative Commons Attribution 4.0 International
      •5•0•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

    • tinker-hp

      Public
      Tinker-HP: High-Performance Massively Parallel Evolution of Tinker on CPUs & GPUs
      C++
      •
      Other
      •24•0•0•0•Updated Mar 4, 2021Mar 4, 2021

    • westpa_tutorials

      Public
      Tutorials and additional documentation for the WESTPA suite
      Jupyter Notebook
      •22•1•0•0•Updated Mar 1, 2021Mar 1, 2021

    • journal_information

      Public
      Information and documents supporting the work of the Living Journal of Computational Molecular Sciences (LiveCoMS)
      sciencepublishingpreprintsjournalsscience-researchscience-journal
      TeX
      •4•8•13•0•Updated Oct 12, 2020Oct 12, 2020

    • DNA_salt_livecoms

      Public
      Lessons learned in atomistic simulation of double-stranded DNA: Solvation and salt concerns.
      TeX
      •1•0•0•0•Updated Dec 2, 2019Dec 2, 2019

    • delphi_tutorial_livecoms

      Public
      TeX
      •2•0•0•0•Updated Nov 25, 2019Nov 25, 2019

    • PMF_Artifacts_LessonsLearned_LiveCoMS

      Public
      Lessons Learned document about PMF artifacts to be submitted to the Living Journal of Computational Molecular Science
      TeX
      •1•0•0•0•Updated Nov 21, 2019Nov 21, 2019

    • gmx_tutorials_livecoms

      Public
      LiveCoMS GROMACS Tutorials Paper
      TeX
      •
      Creative Commons Attribution 4.0 International
      •43•0•0•0•Updated Jun 28, 2019Jun 28, 2019

    • pyemma_tutorials

      Public
      How to analyze molecular dynamics data with PyEMMA
      Jupyter Notebook
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      Creative Commons Attribution 4.0 International
      •35•0•0•0•Updated May 29, 2019May 29, 2019

    • TransportCheckList

      Public
      TeX
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      Creative Commons Attribution 4.0 International
      •2•0•0•0•Updated Jan 8, 2019Jan 8, 2019

    • best_practice_membranes

      Public
      Best Practices document to be submitted to the Living Journal of Computational Molecular Science
      TeX
      •
      Creative Commons Attribution 4.0 International
      •2•0•0•0•Updated Jan 8, 2019Jan 8, 2019

    • basic_simulation_training

      Public
      A document for the Living Journal of Computational Molecular Science (LiveCoMS) which describes basic training for molecular simulations (oriented towards molecular dynamics (MD)), providing some training itself and linking out to other helpful information elsewhere. The intent is that this provide information on the prerequisites which will be …
      TeX
      •
      Creative Commons Attribution 4.0 International
      •19•0•0•0•Updated Dec 29, 2018Dec 29, 2018

    • software-physical-validation

      Public
      Best Practices article (intended for LiveCoMS) treating simulation software validation and physical validation
      TeX
      •
      Other
      •2•0•0•0•Updated Sep 1, 2017Sep 1, 2017

    • Sampling-Uncertainty

      Public
      Best Practices article intended for LiveCoMS
      5•2•0•0•Updated Aug 28, 2017Aug 28, 2017