MD 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

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