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* Chemistry Department, Molecular Biology & Biochemistry Department, and Molecular Biophysics Program, Wesleyan University, Middletown, Connecticut 06459 USA; Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037 USA; Departments of Medicinal Chemistry and of Pharmaceutics and Pharmaceutical Chemistry, University of Utah, Salt Lake City, Utah 84112-5820 USA; Laboratoire de Biochimie Theorique, Institut de Biologie Physico-Chimique, Paris 75005, France; ¶ Physiology and Biophysics, Mount Sinai School of Medicine, New York, New York 10029 USA; || J. Heyrovsky Institute and Center for Complex Molecular Systems and Biomolecules, 182 23 Prague, Czech Republic; ** Institute of Mathematics B, Swiss Federal Institute of Technology, CH 1015 Lausanne, Switzerland; Theoretical Biophysics Group, Max Delbrück Center, D-13122 Berlin, Germany; and Molecular and Cell Biology, University of California-Berkeley, Berkeley California 94720-3202 USA
Correspondence: Address reprint requests to David L. Beveridge, E-mail: dbeveridge{at}wesleyan.edu.
We describe herein a computationally intensive project aimed at carrying out molecular dynamics (MD) simulations including water and counterions on B-DNA oligomers containing all 136 unique tetranucleotide base sequences. This initiative was undertaken by an international collaborative effort involving nine research groups, the "Ascona B-DNA Consortium" (ABC). Calculations were carried out on the 136 cases imbedded in 39 DNA oligomers with repeating tetranucleotide sequences, capped on both ends by GC pairs and each having a total length of 15 nucleotide pairs. All MD simulations were carried out using a well-defined protocol, the AMBER suite of programs, and the parm94 force field. Phase I of the ABC project involves a total of 
0.6 µs of simulation for systems containing 24,000 atoms. The resulting trajectories involve 600,000 coordinate sets and represent 400 gigabytes of data. In this article, the research design, details of the simulation protocol, informatics issues, and the organization of the results into a web-accessible database are described. Preliminary results from 15-ns MD trajectories are presented for the d(CpG) step in its 10 unique sequence contexts, and issues of stability and convergence, the extent of quasiergodic problems, and the possibility of long-lived conformational substates are discussed.
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