International Tables for Crystallography (2006). Vol. F, ch. 20.2, pp. 489-495   | 1 | 2 |
doi: 10.1107/97809553602060000706

Chapter 20.2. Molecular-dynamics simulations of biological macromolecules

Contents

  • 20.2. Molecular-dynamics simulations of biological macromolecules  (pp. 489-495) | html | pdf | chapter contents |
    • 20.2.1. Introduction  (p. 489) | html | pdf |
    • 20.2.2. The simulation method  (p. 489) | html | pdf |
    • 20.2.3. Potential-energy function  (pp. 489-491) | html | pdf |
      • 20.2.3.1. Empirical energy  (pp. 489-490) | html | pdf |
      • 20.2.3.2. Particle mesh Ewald  (p. 490) | html | pdf |
      • 20.2.3.3. Experimental restraints in the energy function  (pp. 490-491) | html | pdf |
    • 20.2.4. Empirical parameterization of the force field  (p. 491) | html | pdf |
    • 20.2.5. Modifications in the force field for structure determination  (p. 491) | html | pdf |
    • 20.2.6. Internal dynamics and average structures  (p. 491) | html | pdf |
    • 20.2.7. Assessment of the simulation procedure  (p. 492) | html | pdf |
    • 20.2.8. Effect of crystallographic atomic resolution on structural stability during molecular dynamics  (pp. 492-494) | html | pdf |
    • References | html | pdf |
    • Figures
      • Fig. 20.2.7.1. Structural comparison and radii of gyration of various proteins as a function of time in the molecular-dynamics simulation  (p. 492) | html | pdf |
      • Fig. 20.2.8.1. Cα tracings of BPTI  (p. 493) | html | pdf |
      • Fig. 20.2.8.2. BPTI r.m.s. coordinate differences between the energy-minimized crystallographic structure and MD snapshots from three simulations  (p. 493) | html | pdf |
    • Tables
      • Table 20.2.8.1. R.m.s. coordinate differences between crystallographic structures and average MD structures  (p. 493) | html | pdf |