irrelevant2021 / MDNotebooks

Jupyter Notebooks for Molecular Dynamics

MDNotebooks

Molecular Dynamics made easy with Jupyter Notebook.

All the Gromacs commands, result analysis, plotting could be carried out using single Jupyter Notebook with the support of Gromacs software and other python libraries.

Tutorials are taken from

Justin A. Lemkul, Ph.D. Virginia Tech Department of Biochemistry - http://www.mdtutorials.com/

Install anaconda from the web - https://www.anaconda.com/products/individual

Install Gromacs from the web or run - conda install -c bioconda gromacs

Install libraries - conda install nglview mdanalysis

Install additional libraries - pip install GromacsWrapper pytraj