Comparison of different schemes to treat long-range electrostatic interactions in molecular dynamics simulations of a protein crystal.
Eight molecular dynamics simulations of a ubiquitin crystal unit cell were performed to investigate the effect of different schemes to treat the long-range electrostatic interactions as well as the need to include counter ions. A crystal system was chosen as the test system, because the higher charge density compared with a protein in solution makes it more sensitive to the way of treating the electrostatic interactions. Three different schemes of treating the long-range interactions were compared: straight cutoff, reaction-field approximation, and a lattice-sum method (P3M). For each of these schemes, two simulations were performed, one with and one without the counter ions. Two additional simulations with a reaction-field force and different initial placements of the counter ions were performed to examine the effect of the initial positions of the ions. The inclusion of long-range electrostatic interactions using either a reaction-field or a lattice-sum method proved to be necessary for the simulation of crystals. These two schemes did not differ much in their ability to reproduce the crystallographic structure. The inclusion of counter ions, on the other hand, seems not necessary for obtaining a stable simulation. The initial positions of the ions have a visible but small effect on the simulation.
Walser
R
R
Laboratory of Physical Chemistry, Swiss Federal Institute of Technology Zürich, Zürich, Switzerland.
Hünenberger
P H
PH
van Gunsteren
W F
WF
D000595:Amino Acid Sequence; D003198:Computer Simulation; D003460:Crystallization; D004058:Diffusion; D006863:Hydrogen-Ion Concentration; D008958:Models, Molecular; D017433:Protein Structure, Secondary; D011522:Protons; D055672:Static Electricity; D013816:Thermodynamics; D013997:Time Factors; D014452:Ubiquitins
D011522:Protons; D014452:Ubiquitins