Continuous Tempering Molecular Dynamics: A Deterministic Approach to Simulated Tempering

Lenner, Nicolas und Mathias, Gerald (2016): Continuous Tempering Molecular Dynamics: A Deterministic Approach to Simulated Tempering. In: Journal of Chemical theory and Computation, Bd. 12, Nr. 2: S. 486-498

Abstract

Continuous tempering molecular dynamics (CTMD) generalizes simulated tempering (ST) to a continuous temperature space. Opposed to ST the CTMD equations of motion are fully deterministic and feature a conserved quantity that can be used to validate the simulation. Three variants of CTMD are discussed and compared by means of a simple test system. The implementation features of the most stable and simplest variant CTMD-U in the program package IPHIGENIE are described. Two applications alanine dipeptide (Ac-Ala-NHMe) in explicit water and octa-alanine (Ac-(Ala)8-NHMe) simulated in a dielectric continuum demonstrate the functionality of CTMD-U. Furthermore;they serve to evaluate its sampling efficiency. Here, CTMD-U outperforms ST by 35% and replica exchange even by 75%.

• Dokumententyp: Zeitschriftenartikel
• Fakultät: Physik
• Themengebiete: 500 Naturwissenschaften und Mathematik > 530 Physik
• ISSN: 1549-9618
• Sprache: Englisch