Vectorization of the generalized Born model for molecular dynamics on shared-memory computers

Carlos P. Sosa, Tom Hewitt, Matthew R. Lee, David A. Case

Research output: Contribution to journalArticlepeer-review

7 Scopus citations


Vectorization and performance of the generalized Born solvation model (GB) as it is implemented in the AMBER program is presented in this study. Nonbonded interactions computed within the generalized Born model use the pairwise approximation of Hawkins et al. [J. Phys. Chem. 100 (1996) 19,824], which is in turn a variant of the model proposed by Schaeffer and Froemmel [J. Mol. Biol. 216 (1990) 1045]. The performance of this implementation on CRAY SV1 vector machines is discussed with reference to several proteins. Loop vectorization has shown improvements by as much as a factor of 10. Comparison of the timings of the GB method against simulations using fully hydrated proteins favors the GB method.

Original languageEnglish (US)
Pages (from-to)193-201
Number of pages9
JournalJournal of Molecular Structure: THEOCHEM
Issue number1-2
StatePublished - Aug 6 2001
Externally publishedYes

All Science Journal Classification (ASJC) codes

  • Biochemistry
  • Condensed Matter Physics
  • Physical and Theoretical Chemistry


  • CRAY SV1
  • Generalized Born
  • Molecular dynamics
  • Vector


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