BAR-based optimum adaptive steered MD for configurational sampling

Xiaohui Wang, Xingzhao Tu, Boming Deng, John Zhang, Zhaoxi Sun

Research output: Contribution to journalArticle

Abstract

The equilibrium and nonequilibrium adaptive alchemical free energy simulation methods optimum Bennett's acceptance ratio and optimum crooks' equation (OCE), based on the statistically optimal bidirectional reweighting estimator named Bennett's Acceptance Ratio or Crooks' equation, perform initial sampling in the staging alchemical transformation and then determine the importance rank of different states via the time-derivative of the variance. The method is proven to give speedups compared with the equal time rule. In the current work, we extend the time derivative of variance guided adaptive sampling method to the configurational space, falling in the term of steered MD (SMD). The SMD approach biasing physically meaningful collective variable (CV) such as one dihedral or one distance to pulling the system from one conformational state to another. By minimizing the variance of the free energy differences along the pathway in an optimized way, a new type of adaptive SMD (ASMD) is introduced. As exhibits in the alchemical case, this adaptive sampling method outperforms the traditional equal-time SMD in nonequilibrium stratification. Also, the method gives much more efficient calculation of potential of mean force than the selection criterion-based ASMD scheme, which is proven to be more efficient than traditional SMD. The OCE workflow is periodicity-of-CV dependent while ASMD is not. The performance is demonstrated in a dihedral flipping case and two distance pulling cases, accounting for periodic and nonperiodic CVs, respectively.

Original languageEnglish (US)
JournalJournal of Computational Chemistry
DOIs
StatePublished - Jan 1 2019

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Surface mount technology
Sampling
Adaptive Sampling
Free energy
Adaptive Method
Sampling Methods
Non-equilibrium
Derivatives
Free Energy
Derivative
Energy Method
Stratification
Simulation Methods
Periodicity
Work Flow
Pathway
Estimator
Dependent
Term

Keywords

  • adaptive sampling
  • adaptive steered molecular dynamics
  • bidirectional reweighting
  • Deca-alanine
  • dihedral flipping
  • free energy profile
  • free energy simulation
  • nonequilibrium thermodynamics
  • statistically optimal
  • steered molecular dynamics

ASJC Scopus subject areas

  • Chemistry(all)
  • Computational Mathematics

Cite this

BAR-based optimum adaptive steered MD for configurational sampling. / Wang, Xiaohui; Tu, Xingzhao; Deng, Boming; Zhang, John; Sun, Zhaoxi.

In: Journal of Computational Chemistry, 01.01.2019.

Research output: Contribution to journalArticle

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