MolModEdu

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

Contents

1. Molecular Dynamics Simulations

   • Course and educational materials
   • Tutorials
   • Code examples and templates
     • Gromacs
     • NAMD
     • MDanalysis

2. Protein structure prediction

   • Homology modeling using MODELLER
   • Rosetta
   • Diffrent servers - I-TASSER, Robetta, RaptorX

3. Miscellaneous

   • Phenix

Molecular Dynamics Simulations

MD: Courses and educational materials

• Overview lecture by Alexey K. Shaytan

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

• The recommended way for setting up an in-house MD simulation is to use the extensive gmx_template (currently available only locally), ideally in conjunction with the customly created moldyn conda environment on Newton linux cluster and bindings to Lomonosov-2 supercomputer.
• A quick example of using Jupyter notebooks and MDAnalysis for preparing and running MD in GROMACS
• Molecular dynamics simulation of biomembranes at different temperature

Gromacs Resources

• Gromacs force fileds https://github.com/intbio/gromacs_ff
• Typical Gromacs MDP files and protocols https://github.com/intbio/gmx_protocols
• Gromacs packed in conda package manager https://github.com/intbio/gromacs-conda

NAMD

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

MDAnalysis

• A quick example of using Jupyter notebooks and MDAnalysis for preparing and running MD in GROMACS

Homology modeling using MODELLER

• MODELLER examples

PHENIX - Molecular modeling for X-ray crystallography

https://www.phenix-online.org

• Minimizing molecular geometry using phenix