ArticleBiophysical journal1998
Structural equilibrium of DNA represented with different force fields.
Article in Biophysical journal, 1998. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed.
- Benchmark assessment of molecular geometries and energies from small molecule force fields.F1000Research · 2020Article
- Molecular dynamics simulations of a DMSO/water mixture using the AMBER force field.Journal of molecular modeling · 2018Article
- Multivalent ion-mediated nucleic acid helix-helix interactions: RNA versus DNA.Nucleic acids research · 2015Article
- Close encounters with DNA.Journal of physics. Condensed matter : an Institute of Physics journal · 2014Review
- Role of histone tails in structural stability of the nucleosome.PLoS computational biology · 2011Article
- Evaluation of DNA Force Fields in Implicit Solvation.Journal of chemical theory and computation · 2011Article
- Temperature-induced melting of double-stranded DNA in the absence and presence of covalently bonded antitumour drugs: insight from molecular dynamics simulations.Nucleic acids research · 2011Article
- Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles.Journal of chemical theory and computation · 2011Article
- A model for Structure and Thermodynamics of ssDNA and dsDNA Near a Surface: a Coarse Grained Approach.Computer physics communications · 2010Article
- The pathway of oligomeric DNA melting investigated by molecular dynamics simulations.Biophysical journal · 2008Article
- Strain softening in stretched DNA.Physical review letters · 2008Article
- Probing the interactions of the solvated electron with DNA by molecular dynamics simulations: bromodeoxyuridine substituted DNA.Journal of molecular modeling · 2008Article
- Atomic-level simulations of seeman DNA nanostructures: the paranemic crossover in salt solution.Biophysical journal · 2006Article
- The effect of salt concentration on DNA conformation transition: a molecular-dynamics study.Journal of molecular modeling · 2006Article
- The B- to A-DNA transition and the reorganization of solvent at the DNA surface.Biophysical journal · 2005Article
- The physical determinants of the DNA conformational landscape: an analysis of the potential energy surface of single-strand dinucleotides in the conformational space of duplex DNA.Nucleic acids research · 2005Article
- Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. I. Research design and results on d(CpG) steps.Biophysical journal · 2004Article
- The stability of Seeman JX DNA topoisomers of paranemic crossover (PX) molecules as a function of crossover number.Nucleic acids research · 2004Article
- Formation pathways of a guanine-quadruplex DNA revealed by molecular dynamics and thermodynamic analysis of the substates.Biophysical journal · 2003Article
- DNA polymorphism: a comparison of force fields for nucleic acids.Biophysical journal · 2003Article
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2 authors.
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No grant is acknowledged in the PubMed record.
Abstract
We have recently indicated preliminary evidence of different equilibrium average structures with the CHARMM and AMBER force fields in explicit solvent molecular dynamics simulations on the DNA duplex d(C5T5) . d(A5G5) (Feig, M. and B.M. Pettitt, 1997, Experiment vs. Force Fields: DNA conformation from molecular dynamics simulations. J. Phys. Chem. B. (101:7361-7363). This paper presents a detailed comparison of DNA structure and dynamics for both force fields from extended simulation times of 10 ns each. Average structures display an A-DNA base geometry with the CHARMM force field and a base geometry that is intermediate between A- and B-DNA with the AMBER force field. The backbone assumes B form on both strands with the AMBER force field, while the CHARMM force field produces heterogeneous structures with the purine strand in A form and the pyrimidine strand in dynamical equilibrium between A and B conformations. The results compare well with experimental data for the cytosine/guanine part but fail to fully reproduce an overall B conformation in the thymine/adenine tract expected from crystallographic data, particularly with the CHARMM force field. Fluctuations between A and B conformations are observed on the nanosecond time scale in both simulations, particularly with the AMBER force field. Different dynamical behavior during the first 4 ns indicates that convergence times of several nanoseconds are necessary to fully establish a dynamical equilibrium in all structural quantities on the time scale of the simulations presented here.
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