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Hédin F, Plattner N, Doll JD, et al. Spatial Averaging: Sampling Enhancement for Exploring Configurational Space of Atomic Clusters and Biomolecules. J Chem Theory Comput. 2014;10(10):4284-96doi: 10.1021/ct500529w.
Hédin, F., Plattner, N., Doll, J. D., & Meuwly, M. (2014). Spatial Averaging: Sampling Enhancement for Exploring Configurational Space of Atomic Clusters and Biomolecules. Journal of chemical theory and computation, 10(10), 4284-96. https://doi.org/10.1021/ct500529w
Hédin, Florent, et al. "Spatial Averaging: Sampling Enhancement for Exploring Configurational Space of Atomic Clusters and Biomolecules." Journal of chemical theory and computation vol. 10,10 (2014): 4284-96. doi: https://doi.org/10.1021/ct500529w
Hédin F, Plattner N, Doll JD, Meuwly M. Spatial Averaging: Sampling Enhancement for Exploring Configurational Space of Atomic Clusters and Biomolecules. J Chem Theory Comput. 2014 Oct 14;10(10):4284-96. doi: 10.1021/ct500529w. PMID: 26588125.
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J Chem Theory Comput. 2014 Oct 14;10(10):4284-96. doi: 10.1021/ct500529w.

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

Journal of chemical theory and computation

Florent Hédin, Nuria Plattner, J D Doll, Markus Meuwly

Affiliations

  1. Department of Chemistry, University of Basel , Klingelbergstrasse 80, CH-4056 Basel, Switzerland.
  2. Department of Mathematics and Computer Science, Freie Universität Berlin , Arnimallee 6, D-14195 Berlin, Germany.
  3. Department of Chemistry, Brown University , Providence, Rhode Island 02912, United States.

PMID: 26588125 DOI: 10.1021/ct500529w

Abstract

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.

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