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Educational Notes on Molecular Modeling

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

## Contents
1. [**Molecular Dynamics Simulations**](#MD) 
   + [Course and educational materials](#MDpresent)
   + [Tutorials](#MDtutorials)
   + [Code examples and templates](#MDcode)
        - [Gromacs](#MDcode_gromacs)
        - [NAMD](#MDcode_namd)
        - [MDanalysis](#MDcode_mdanalysis)
        
2. Protein structure prediction
   + [Homology modeling using MODELLER](#modeller)
   + Rosetta
   + Diffrent servers - I-TASSER, Robetta, RaptorX
 
 
3. Miscellaneous
   + [Phenix](#phenix)

## Molecular Dynamics Simulations

### MD: Courses and educational materials
- [Overview lecture by Alexey K. Shaytan](https://www.dropbox.com/s/y971h41by5wz0io/md_presentation.pptx?dl=0)

### 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](GROMACS/beginner)
2. [An in-depth Gromacs MD tutorial: simulating nucleosome dynamics. GROMACS/nucl](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]( https://github.com/intbio/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](MDanalysis/Nucleosome_dimer_MD_preparation.ipynb)
- [Molecular dynamics simulation of biomembranes at different temperature](https://github.com/intbio/MolModEdu/tree/master/GROMACS/biomembrane)

##### 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](https://www.ncbi.nlm.nih.gov/pubmed/26699921) - [here](MD/NAMD/nucl).

#### MDAnalysis
- [A quick example of using Jupyter notebooks and MDAnalysis for preparing and running MD in GROMACS](MDanalysis/Nucleosome_dimer_MD_preparation.ipynb)

## Homology modeling using MODELLER
- [MODELLER examples](MODELLER/examples.ipynb)

## PHENIX - Molecular modeling for X-ray crystallography
[https://www.phenix-online.org](https://www.phenix-online.org)
- [Minimizing molecular geometry using phenix](phenix/geo_minim.md)

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