title: Continuous Tempering Molecular Dynamics: A Deterministic Approach to Simulated Tempering.
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%.
authors.affiliation: Lehrstuhl für BioMolekulare Optik, Ludwig-Maximilians Universität München , Oettingenstrasse 67, 80538 München, Germany.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Lenner
authors.affiliation: Lehrstuhl für BioMolekulare Optik, Ludwig-Maximilians Universität München , Oettingenstrasse 67, 80538 München, Germany.
authors.forename: Gerald
authors.initials: G
authors.lastname: Mathias
mesh_terms: D000409:Alanine / Q000031:analogs & derivatives / Q000737:chemistry; D000465:Algorithms; D056004:Molecular Dynamics Simulation; D009842:Oligopeptides / Q000737:chemistry; D013696:Temperature; D014867:Water / Q000737:chemistry
chemical_list: D009842:Oligopeptides; D014867:Water; C024314:N-acetylalanyl-N-methylamide; D000409:Alanine