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MolModEdu

Educational/Research Materials on Molecular Modeling: Tutorials, Code Examples and Templates, Resources, Course Materials

Contents

  1. Molecular Dynamics Simulations

  2. Protein structure prediction

  3. Miscellaneous

Molecular Dynamics Simulations

MD: Courses and educational materials

MD: Tutorials

General introduction to MD

Here we offer two tutorials, a quick one for beginners and an in-depth one. The first one is indended to be as simple as possible with detailed instuctions, the second one requires more technical skills and independent work.

  1. A basic beginner's tutorial on MD simulations in Gromacs
  2. An in-depth Gromacs MD tutorial: simulating nucleosome dynamics. GROMACS/nucl

MD: Code examples and templates

Gromacs

Gromacs Resources

NAMD

  • Example of a pipeline to simulate nucleosome dynamics and perform trajectory analysis from JMB paper - here.

MDAnalysis

Homology modeling using MODELLER

PHENIX - Molecular modeling for X-ray crystallography

https://www.phenix-online.org

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Educational Notes on Molecular Modeling

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