Chapter 20.1 Molecular-dynamics simulation of protein crystals: convergence of molecular properties of ubiquitin

Crystallography of biological macromolecules

Second Online Edition (2012)

Part 20. Energy calculations and molecular dynamics

  1. U. Stocker,
  2. W. F. van Gunsteren

Published Online: 14 APR 2012

DOI: 10.1107/97809553602060000877

International Tables for Crystallography

International Tables for Crystallography

How to Cite

Stocker, U. and van Gunsteren, W. F. 2012. Molecular-dynamics simulation of protein crystals: convergence of molecular properties of ubiquitin. International Tables for Crystallography. F:20:20.1:633–641.

Author Information

  1. Laboratory of Physical Chemistry, ETH-Zentrum, 8092 Zürich, Switzerland

Publication History

  1. Published Online: 14 APR 2012


A unit cell of ubiquitin was simulated for 2 ns using molecular dynamics to investigate the degree of convergence of different molecular properties in crystals. Energies, deviation from the experimentally derived crystal structure, atomic positional fluctuations and dihedral-angle fluctuations were analysed. Most of the properties examined are converged after 2 ns. The atomic positional deviation from the X-ray structure had not converged within 2 ns.


  • molecular dynamics;
  • molecular-dynamics simulation;
  • ubiquitin