Experiment vs force fields

DNA conformation from molecular dynamics simulations

Michael Feig, Bernard Pettitt

Research output: Contribution to journalArticle

59 Citations (Scopus)

Abstract

Molecular dynamics simulations of the DNA duplex d(CCCCCTTTTT)2 in ionic solution with AMBER and CHARMM force fields are compared. CHARMM parameters result in an A-DNA conformation with a heterogeneous backbone structure, but in the AMBER force field the DNA is found in a B-like helix with a homogeneous B-DNA backbone during the first 3.5 ns before moving close to the CHARMM structure in the A family at around 4 ns. Both structures are in partial disagreement with experiment, which reports the C/G part in A and the A/T part in B form.

Original languageEnglish (US)
Pages (from-to)7361-7363
Number of pages3
JournalJournal of Physical Chemistry B
Volume101
Issue number38
DOIs
StatePublished - Jan 1 1997
Externally publishedYes

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Conformations
Molecular dynamics
DNA
Computer simulation
Experiments

ASJC Scopus subject areas

  • Engineering(all)

Cite this

Experiment vs force fields : DNA conformation from molecular dynamics simulations. / Feig, Michael; Pettitt, Bernard.

In: Journal of Physical Chemistry B, Vol. 101, No. 38, 01.01.1997, p. 7361-7363.

Research output: Contribution to journalArticle

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