Prerequisites

Software

Biological molecules

Water molecule
AminoAcids
Proteins
DNA and RNA
Molecular systems

MD simulations of protein

MD simulations of calmodulin

MD simulations of small molecules

Create topology and coordinates for benzene molecule
Linear hydrocarbons (alkanes)
GROMACS simulations of a box of 1000 octane molecules

Implementations

Numerical integration of equations of motion
From potential energy to atomic forces
Bonded interactions
Non-bonded interactions
PME
Constraints

Reference

Quick Reference
Instructor’s guide

Home

Three-body potential

MD simulations

Proteins
Edit on GitHub

Proteins

 

Secondary structure

 

Tertiary structure

  

Protein folding

 

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