Two-component multicanonical Monte Carlo method for effective conformation sampling
✍ Scribed by Higo, Junichi; Nakajima, Nobuyuki; Shirai, Hiroki; Kidera, Akinori; Nakamura, Haruki
- Publisher
- John Wiley and Sons
- Year
- 1997
- Tongue
- English
- Weight
- 213 KB
- Volume
- 18
- Category
- Article
- ISSN
- 0192-8651
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✦ Synopsis
A multicanonical algorithm, which is one of the most powerful conformation-sampling methods to obtain the density of states described by a Ž . 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᎐sitespecific energies between helices; and, in the other set, the total potential energy Ž . 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.