Biomolecular free energy profiles by a shooting/umbrella sampling protocol, "BOLAS"

Ravi Radhakrishnan, Tamar Schlick

Research output: Contribution to journalArticle

Abstract

A technique called BOLAS for the computation of free energies corresponding to conformational transitions in complex systems was developed by combining a Monte Carlo ensemble of trajectories generated by the shooting algorithm with umbrella sampling. The technique preserved microscopic reversibility and led to correct equilibrium distribution. The technique enabled the computation of free energy profiles along complex reaction coordinates for biomolecular systems with a lower systematic error compared to traditional, force-biased umbrella sampling protocols. The scope of the technique was demonstrated by applying it to the sugar repuckering transition in a solvated deoxyadenosine molecule.

Original languageEnglish (US)
Pages (from-to)2436-2444
Number of pages9
JournalJournal of Chemical Physics
Volume121
Issue number5
DOIs
StatePublished - Aug 1 2004

Fingerprint

Free energy
sampling
free energy
Sampling
Systematic errors
sugars
profiles
complex systems
Sugars
systematic errors
Large scale systems
Trajectories
trajectories
Molecules
molecules
2'-deoxyadenosine

ASJC Scopus subject areas

  • Atomic and Molecular Physics, and Optics

Cite this

Biomolecular free energy profiles by a shooting/umbrella sampling protocol, "BOLAS". / Radhakrishnan, Ravi; Schlick, Tamar.

In: Journal of Chemical Physics, Vol. 121, No. 5, 01.08.2004, p. 2436-2444.

Research output: Contribution to journalArticle

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