Optimal replica exchange method combined with Tsallis weight sampling
- PMID: 19368436
- PMCID: PMC2736612
- DOI: 10.1063/1.3108523
Optimal replica exchange method combined with Tsallis weight sampling
Abstract
A unified framework integrating the generalized ensemble sampling associated with the Tsallis weight [C. Tsallis, J. Stat. Phys. 52, 479 (1988)] and the replica exchange method (REM) has been proposed to accelerate the convergence of the conventional temperature REM (t-REM). Using the effective temperature formulation of the Tsallis weight sampling, it is shown that the average acceptance probability for configurational swaps between neighboring replicas in the combination of Tsallis weight sampling and REM (Tsallis-REM) is directly proportional to an overlap integral of the energy distributions of neighboring replicas as in the t-REM. Based on this observation, we suggest a robust method to select optimal Tsallis parameters in the conventional parametrization scheme and present new parametrization schemes for the Tsallis-REM, which significantly improves the acceptance of configurational swaps by systematically modulating energy overlaps between neighboring replicas. The distinguished feature of our method is that all relevant parameters in the Tsallis-REM are automatically determined from the equilibrium phase simulation using the t-REM. The overall performance of our method is explicitly demonstrated for various simulation conditions for the Lennard-Jones 31 atom clusters, exhibiting a double-funneled energy landscape.
Figures










Similar articles
-
Replica exchange statistical temperature Monte Carlo.J Chem Phys. 2009 Mar 28;130(12):124112. doi: 10.1063/1.3095422. J Chem Phys. 2009. PMID: 19334813 Free PMC article.
-
Dynamical origin of enhanced conformational searches of Tsallis statistics sampling.J Chem Phys. 2004 Jul 15;121(3):1626-35. doi: 10.1063/1.1763841. J Chem Phys. 2004. PMID: 15260711
-
Generalized simulated tempering realized on expanded ensembles of non-Boltzmann weights.J Chem Phys. 2004 Sep 22;121(12):5590-601. doi: 10.1063/1.1786578. J Chem Phys. 2004. PMID: 15366981
-
Ligand docking simulations by generalized-ensemble algorithms.Adv Protein Chem Struct Biol. 2013;92:63-91. doi: 10.1016/B978-0-12-411636-8.00002-X. Adv Protein Chem Struct Biol. 2013. PMID: 23954099 Review.
-
Influence of various parameters in the replica-exchange molecular dynamics method: Number of replicas, replica-exchange frequency, and thermostat coupling time constant.Biophys Physicobiol. 2018 Aug 8;15:165-172. doi: 10.2142/biophysico.15.0_165. eCollection 2018. Biophys Physicobiol. 2018. PMID: 30250775 Free PMC article. Review.
Cited by
-
Hamiltonian Switch Metropolis Monte Carlo Simulations for Improved Conformational Sampling of Intrinsically Disordered Regions Tethered to Ordered Domains of Proteins.J Chem Theory Comput. 2014 Aug 12;10(8):3550-3562. doi: 10.1021/ct5002297. Epub 2014 Jun 3. J Chem Theory Comput. 2014. PMID: 25136274 Free PMC article.
-
Replica exchange statistical temperature molecular dynamics algorithm.J Phys Chem B. 2012 Jul 26;116(29):8646-53. doi: 10.1021/jp300366j. Epub 2012 May 15. J Phys Chem B. 2012. PMID: 22540354 Free PMC article.
-
Generalized replica exchange method.J Chem Phys. 2010 Jun 14;132(22):224107. doi: 10.1063/1.3432176. J Chem Phys. 2010. PMID: 20550390 Free PMC article.
-
Generalized simulated tempering for exploring strong phase transitions.J Chem Phys. 2010 Oct 21;133(15):154101. doi: 10.1063/1.3503503. J Chem Phys. 2010. PMID: 20969364 Free PMC article.
-
Replica exchanging self-guided Langevin dynamics for efficient and accurate conformational sampling.J Chem Phys. 2012 Jul 28;137(4):044106. doi: 10.1063/1.4737094. J Chem Phys. 2012. PMID: 22852596 Free PMC article.
References
Publication types
MeSH terms
Grants and funding
LinkOut - more resources
Full Text Sources