Blue Moon sampling, vectorial reaction coordinates, and unbiased constrained dynamics

Giovanni Ciccotti, Raymond Kapral, Eric Vanden Eijnden

Research output: Contribution to journalArticle

Abstract

We give a new formula expressing the components of the mean force in terms of a conditional expectation which can be computed by Blue Moon sampling. This generalizes to the vectorial case a formula first derived by Ruiz-Montero et al. [Mol. Phys. 1997, 90, 925] for a scalar reaction coordinate. We also discuss how to compute this conditional average by means of constrained stochastic dynamics which, unlike the usual constrained molecular dynamics, introduces no bias. Finally, we give a new perspective on bias removal by using constrained molecular dynamics.

Original languageEnglish (US)
Pages (from-to)1809-1814
Number of pages6
JournalChemPhysChem
Volume6
Issue number9
DOIs
StatePublished - Sep 5 2005

Fingerprint

Moon
moon
Molecular dynamics
sampling
molecular dynamics
Sampling
scalars

Keywords

  • Blue Moon sampling
  • Constrained stochastics dynamics
  • Free energy
  • Mean force
  • Reaction coordinates

ASJC Scopus subject areas

  • Atomic and Molecular Physics, and Optics

Cite this

Blue Moon sampling, vectorial reaction coordinates, and unbiased constrained dynamics. / Ciccotti, Giovanni; Kapral, Raymond; Vanden Eijnden, Eric.

In: ChemPhysChem, Vol. 6, No. 9, 05.09.2005, p. 1809-1814.

Research output: Contribution to journalArticle

Ciccotti, Giovanni ; Kapral, Raymond ; Vanden Eijnden, Eric. / Blue Moon sampling, vectorial reaction coordinates, and unbiased constrained dynamics. In: ChemPhysChem. 2005 ; Vol. 6, No. 9. pp. 1809-1814.
@article{7c187069f06f4f6b9c0e9973fc87195b,
title = "Blue Moon sampling, vectorial reaction coordinates, and unbiased constrained dynamics",
abstract = "We give a new formula expressing the components of the mean force in terms of a conditional expectation which can be computed by Blue Moon sampling. This generalizes to the vectorial case a formula first derived by Ruiz-Montero et al. [Mol. Phys. 1997, 90, 925] for a scalar reaction coordinate. We also discuss how to compute this conditional average by means of constrained stochastic dynamics which, unlike the usual constrained molecular dynamics, introduces no bias. Finally, we give a new perspective on bias removal by using constrained molecular dynamics.",
keywords = "Blue Moon sampling, Constrained stochastics dynamics, Free energy, Mean force, Reaction coordinates",
author = "Giovanni Ciccotti and Raymond Kapral and {Vanden Eijnden}, Eric",
year = "2005",
month = "9",
day = "5",
doi = "10.1002/cphc.200400669",
language = "English (US)",
volume = "6",
pages = "1809--1814",
journal = "ChemPhysChem",
issn = "1439-4235",
publisher = "Wiley-VCH Verlag",
number = "9",

}

TY - JOUR

T1 - Blue Moon sampling, vectorial reaction coordinates, and unbiased constrained dynamics

AU - Ciccotti, Giovanni

AU - Kapral, Raymond

AU - Vanden Eijnden, Eric

PY - 2005/9/5

Y1 - 2005/9/5

N2 - We give a new formula expressing the components of the mean force in terms of a conditional expectation which can be computed by Blue Moon sampling. This generalizes to the vectorial case a formula first derived by Ruiz-Montero et al. [Mol. Phys. 1997, 90, 925] for a scalar reaction coordinate. We also discuss how to compute this conditional average by means of constrained stochastic dynamics which, unlike the usual constrained molecular dynamics, introduces no bias. Finally, we give a new perspective on bias removal by using constrained molecular dynamics.

AB - We give a new formula expressing the components of the mean force in terms of a conditional expectation which can be computed by Blue Moon sampling. This generalizes to the vectorial case a formula first derived by Ruiz-Montero et al. [Mol. Phys. 1997, 90, 925] for a scalar reaction coordinate. We also discuss how to compute this conditional average by means of constrained stochastic dynamics which, unlike the usual constrained molecular dynamics, introduces no bias. Finally, we give a new perspective on bias removal by using constrained molecular dynamics.

KW - Blue Moon sampling

KW - Constrained stochastics dynamics

KW - Free energy

KW - Mean force

KW - Reaction coordinates

UR - http://www.scopus.com/inward/record.url?scp=24944568819&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=24944568819&partnerID=8YFLogxK

U2 - 10.1002/cphc.200400669

DO - 10.1002/cphc.200400669

M3 - Article

VL - 6

SP - 1809

EP - 1814

JO - ChemPhysChem

JF - ChemPhysChem

SN - 1439-4235

IS - 9

ER -