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 language | English (US) |
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Pages (from-to) | X-7363 |
Journal | Journal of Physical Chemistry B |
Volume | 101 |
Issue number | 38 |
State | Published - Sep 18 1997 |
Externally published | Yes |
ASJC Scopus subject areas
- Physical and Theoretical Chemistry
- Surfaces, Coatings and Films
- Materials Chemistry