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Titolo:
Distance-type reaction coordinates for modelling activated processes
Autore:
Schlitter, J; Swegat, W; Mulders, T;
Indirizzi:
Ruhr Univ Bochum, Lehrstuhl Biophys, D-44780 Bochum, Germany Ruhr Univ Bochum Bochum Germany D-44780 Biophys, D-44780 Bochum, Germany Rhein Westfal TH Aachen, Med Einrichtungen, Inst Biochem, D-52057 Aachen, Germany Rhein Westfal TH Aachen Aachen Germany D-52057 , D-52057 Aachen, Germany Ctr Biophys Mol, F-45071 Orleans, France Ctr Biophys Mol Orleans France F-45071 phys Mol, F-45071 Orleans, France
Titolo Testata:
JOURNAL OF MOLECULAR MODELING
fascicolo: 6, volume: 7, anno: 2001,
pagine: 171 - 177
SICI:
1610-2940(2001)7:6<171:DRCFMA>2.0.ZU;2-Z
Fonte:
ISI
Lingua:
ENG
Soggetto:
CONSTRAINED MOLECULAR-DYNAMICS; FREE-ENERGY; CONFORMATIONAL TRANSITION; STATISTICAL-MECHANICS; COMPUTER-SIMULATION; FORCE; COMPLEXES; SOLVENT;
Keywords:
reaction coordinate; constrained dynamics; targeted molecular dynamics; free energy; thermodynamic integration;
Tipo documento:
Article
Natura:
Periodico
Settore Disciplinare:
Life Sciences
Physical, Chemical & Earth Sciences
Citazioni:
31
Recensione:
Indirizzi per estratti:
Indirizzo: Schlitter, J Ruhr Univ Bochum, Lehrstuhl Biophys, ND 04, D-44780 Bochum, Germany Ruhr Univ Bochum ND 04 Bochum Germany D-44780 ochum, Germany
Citazione:
J. Schlitter et al., "Distance-type reaction coordinates for modelling activated processes", J MOL MODEL, 7(6), 2001, pp. 171-177

Abstract

A suitably defined distance is the simplest parameter for measuring the difference between two positions, orientations, and/or conformations of a molecular system. Distances also provide a first guess for the reaction coordinates of activated processes. It is shown here that mass-weighted distancespossess remarkable mechanical and statistical mechanical properties. They allow us to restrict motions to internal coordinates of a molecule in a simple way where this demand makes sense. Moreover, the computation of free energy changes and rates is facilitated by simple explicit formulae. The numerical treatment of a rate process in a peptide, the ring flip of a phenylalanine, demonstrates the practical application of our results. It also indicates the role of internal friction in macromolecules and the need to consider transmission coefficients.

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Documento generato il 29/03/20 alle ore 23:32:13