Educational/Research Materials on Molecular Modeling: Tutorials, Code Examples and Templates, Resources, Course Materials
Protein structure prediction
- Homology modeling using MODELLER
- Diffrent servers - I-TASSER, Robetta, RaptorX
Molecular Dynamics Simulations
MD: Courses and educational materials
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.
- A basic beginner's tutorial on MD simulations in Gromacs
- An in-depth Gromacs MD tutorial: simulating nucleosome dynamics. GROMACS/nucl
MD: Code examples and templates
- 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
moldynconda 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 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
- Example of a pipeline to simulate nucleosome dynamics and perform trajectory analysis from JMB paper - here.