/simulation

simulation notebooks

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User friendly molecular dynamics simulation combining GROMACS and Google Colab: A complete guide

Flowchart

Notebooks:

  1. Engelberger et al 2021 Open In Colab Simulation using Engelberger et al 2021

  2. Colab MD Simulation Open In Colab Using GROMACS to perform protein in water simulation.

  3. Colab MD Analysis Open In Colab Using MDAnalysis and MDtraj to perform MD trajectory Analysis.

  4. CHARMM-GUI Open In Colab Testing Charmm-gui.

Summary

This Github repository is opened to facilitate Molecular Dynamics (MD) simulations using GROMACS. It serves as an adaptable jupyter notebook for conducting MD simulations and accompanies the supplimentary file for the follwoing Article:

Molecular Dynamics Simulation of Wild and Mutant PSMB8 Protein Using Google Collaboratory Framework: Implications for the Restoration of Inflammation in Experimental Autoimmune Encephalomyelitis (EAE) Pathogenesis** ([link here](link will be updated asap)).

Repository link: ColabMDA

https://github.com/paulshamrat/simulation

Note and Acknowledgement:

We would like to thanks the authors who developed jupyter notebook framework for molecular dynamics simulation on google colab. Please always refer the original GROMACS manual for the simulaiton guide. We are grateful to the Authors of the follwoing article which made possible to adapt this md simulation protocol.

  • F. Engelberger et al 2021; doi: 10.1021/acs.jchemed.1c00022.
  • J. A. Lemkul et al 2018: doi: 10.33011/LIVECOMS.1.1.5068.
  • P. R. Arantes et al 2021: doi: 10.1021/acs.jcim.1c00998.
  • R. J. Gowers et al 2016; doi: 10.25080/majora-629e541a-00e.
  • M. J. Abraham et al 2015; doi: 10.1016/j.softx.2015.06.001

All these datasets are related to Dataset of Molecular Dynamics Simulations for the Upregulated Biomarker PSMB8: 3UNF and its G210V Mutant in Experimental Autoimmune Encephalomyelitis.

DOI

Tested on: 2023-07-17