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Continuous Tempering Molecular Dynamics: A Deterministic Approach to Simulated Tempering
- Source :
- Journal of Chemical Theory and Computation; February 2016, Vol. 12 Issue: 2 p486-498, 13p
- Publication Year :
- 2016
-
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-Uin the program package Iphigenieare 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-Uoutperforms ST by 35% and replica exchange even by 75%.
Details
- Language :
- English
- ISSN :
- 15499618 and 15499626
- Volume :
- 12
- Issue :
- 2
- Database :
- Supplemental Index
- Journal :
- Journal of Chemical Theory and Computation
- Publication Type :
- Periodical
- Accession number :
- ejs38224302
- Full Text :
- https://doi.org/10.1021/acs.jctc.5b00751