Molecular dynamics simulations

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
• Implementation of a simple molecular dynamics code: NaCl in vacuum

Exercises

• Вариант 1: Упаковка ДНК
• Вариант 2: Реакция полимеризации

Reference

• Quick Reference
• Instructor’s guide

Who is the course for?

About the course

See also

MIPT materials

Credits