Stochastic dynamics simulations of the alanine dipeptide using a solvent-modified potential energy surface

Paul E. Smith, Bernard Pettitt, Martin Karplus

Research output: Contribution to journalArticle

62 Citations (Scopus)

Abstract

Langevin dynamics on a potential of mean force energy surface is used to model the effects of aqueous solvent on the structure and dynamics of the alanine dipeptide. Conformational transition rates obtained by correlation function analysis and hazard plots from several simulations are compared. In particular, averages obtained over three 25-ns runs are compared with a single run of 100 ns. Rate constants for selected conformational transitions are also examined. For the conformational processes considered here (α to β and the reverse), we observe two rates, one of which is only significant for simulations of more than 25 ns. On further decomposition of the rate process, it is shown that the two observed rates correspond to the individual rates for rotation around the φ and ψ dihedrals. It is also shown that, for the conformational transitions investigated here, the transition process corresponds to an essentially uncorrelated motion of the two dihedral angles.

Original languageEnglish
Pages (from-to)6907-6913
Number of pages7
JournalJournal of Physical Chemistry
Volume97
Issue number26
StatePublished - 1993
Externally publishedYes

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Potential energy surfaces
Dipeptides
alanine
Alanine
potential energy
Computer simulation
Dihedral angle
Interfacial energy
Rate constants
Hazards
simulation
Decomposition
hazards
surface energy
dihedral angle
plots
decomposition

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry

Cite this

Stochastic dynamics simulations of the alanine dipeptide using a solvent-modified potential energy surface. / Smith, Paul E.; Pettitt, Bernard; Karplus, Martin.

In: Journal of Physical Chemistry, Vol. 97, No. 26, 1993, p. 6907-6913.

Research output: Contribution to journalArticle

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