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
Published Online: 14 APR 2012
© International Union of Crystallography 2006
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.
- 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;