ISSN:
0192-8651
Keywords:
Chemistry
;
Theoretical, Physical and Computational Chemistry
Source:
Wiley InterScience Backfile Collection 1832-2000
Topics:
Chemistry and Pharmacology
,
Computer Science
Notes:
A multicanonical algorithm, which is one of the most powerful conformation-sampling methods to obtain the density of states described by a component (i.e., the total potential energy), was extended to obtain the density of states described by two components. This method was tested on a simplified model for bacteriorhodopsin, which is a membrane protein consisting of seven helices. Two kinds of simulation were done by adopting different sets of two components: in one set, the components were the site-specific and the non-site-specific energies between helices; and, in the other set, the total potential energy and the end-to-end distance (distance between the first and the seventh helices) were used. In both simulations, a wide and flat probability distribution was obtained, showing the efficiency of the two-component method. A variety of applications may be possible by effectively selecting the two components, such as the van der Waals and electrostatic energies, the intermolecular and intramolecular interactions, the solute-solute and solute-solvent interactions, or an energy and a reaction coordinate. © 1997 John Wiley & Sons, Inc. J Comput Chem 18: 2086-2092, 1997
Additional Material:
7 Ill.
Type of Medium:
Electronic Resource
