Comparing generalized ensemble methods for sampling of systems with many degrees of freedom
| Autor: | Sukanya Sasmal, Teresa Head-Gordon, James Lincoff |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2016 |
| Předmět: |
0301 basic medicine
Standard conditions for temperature and pressure General Physics and Astronomy Bioengineering 01 natural sciences 03 medical and health sciences ARTICLES Software Engineering Computational chemistry 0103 physical sciences Statistical physics Physical and Theoretical Chemistry Scaling Chemical Physics 010304 chemical physics business.industry Chemistry Replica Sampling (statistics) Ensemble learning 030104 developmental biology Rate of convergence Phase space Physical Sciences Chemical Sciences business |
| Zdroj: | Lincoff, J; Sasmal, S; & Head-Gordon, T. (2016). Comparing generalized ensemble methods for sampling of systems with many degrees of freedom. Journal of Chemical Physics, 145(17). doi: 10.1063/1.4965439. UC Berkeley: Retrieved from: http://www.escholarship.org/uc/item/0ng8c2q2 The Journal of chemical physics, vol 145, iss 17 |
| DOI: | 10.1063/1.4965439. |
| Popis: | © 2016 Author(s). We compare two standard replica exchange methods using temperature and dielectric constant as the scaling variables for independent replicas against two new corresponding enhanced sampling methods based on non-equilibrium statistical cooling (temperature) or descreening (dielectric). We test the four methods on a rough 1D potential as well as for alanine dipeptide in water, for which their relatively small phase space allows for the ability to define quantitative convergence metrics. We show that both dielectric methods are inferior to the temperature enhanced sampling methods, and in turn show that temperature cool walking (TCW) systematically outperforms the standard temperature replica exchange (TREx) method. We extend our comparisons of the TCW and TREx methods to the 5 residue met-enkephalin peptide, in which we evaluate the Kullback-Leibler divergence metric to show that the rate of convergence between two independent trajectories is faster for TCW compared to TREx. Finally we apply the temperature methods to the 42 residue amyloid-β peptide in which we find non-negligible differences in the disordered ensemble using TCW compared to the standard TREx. All four methods have been made available as software through the OpenMM Omnia software consortium (http://www.omnia.md/). |
| Databáze: | OpenAIRE |
| Externí odkaz: |
|