Experiment vs force fields

DNA conformation from molecular dynamics simulations

Michael Feig, Bernard Pettitt

Research output: Contribution to journalArticle

12 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
JournalJournal of Physical Chemistry B
Volume101
Issue number38
StatePublished - Sep 18 1997
Externally publishedYes

Fingerprint

field theory (physics)
Conformations
Molecular dynamics
DNA
A-Form DNA
deoxyribonucleic acid
B-Form DNA
molecular dynamics
Computer simulation
simulation
Experiments
helices

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry

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, 18.09.1997.

Research output: Contribution to journalArticle

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