Spatial Averaging: Sampling Enhancement for Exploring Configurational Space of Atomic Clusters and Biomolecules

Hedin, Florent and Plattner, Nuria and Doll, J. D. and Meuwly, Markus. (2014) Spatial Averaging: Sampling Enhancement for Exploring Configurational Space of Atomic Clusters and Biomolecules. Journal of Chemical Theory and Computation, 10 (10). pp. 4284-4296.

Full text not available from this repository.

Official URL: http://edoc.unibas.ch/dok/A6338883

Downloads: Statistics Overview


Spatial averaging Monte Carlo (SA-MC) is an efficient algorithm dedicated to the study of rare-event problems. At the heart of this method is the realization that from the equilibrium density a related, modified probability density can be constructed through a suitable transformation. This new density is more highly connected than the original density, which increases the probability for transitions between neighboring states, which in turn speeds up the sampling. The first successful investigations included the diffusion of small molecules in condensed phase environments and characterization of the metastable states of the migration of the CO ligand in myoglobin. In the present work, a general and robust implementation including rotational and torsional moves in the CHARMM molecular modeling software is introduced. Also, a procedure to estimate unbiased properties is proposed in order to compute thermodynamic observables. These procedures are suitable to study a range of topical systems including Lennard-Jones clusters of different sizes and the blocked alanine dipeptide (Ala)(2) in implicit and explicit solvent. In all cases, SA-MC is found to outperform standard Metropolis simulations in sampling configurational space at little extra computational expense. The results for (Ala)(2) in explicit solvent are in good agreement with previous umbrella sampling simulations.
Faculties and Departments:05 Faculty of Science > Departement Chemie > Chemie > Physikalische Chemie (Meuwly)
UniBasel Contributors:Meuwly, Markus
Item Type:Article, refereed
Article Subtype:Research Article
Publisher:American Chemical Society
Note:Publication type according to Uni Basel Research Database: Journal article
Identification Number:
Last Modified:07 Dec 2016 12:03
Deposited On:06 Feb 2015 09:59

Repository Staff Only: item control page