Vectorization and performance of the generalized Born solvation model (GB)
as it is implemented in the AMBER program is presented in this study. Nonbo
nded interactions computed within the generalized Born model use the pairwi
se approximation of Hawkins et al. [J. Phys. Chem. 100 (1996) 19,824], whic
h 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. Comparis
on of the timings of the GB method against simulations using fully hydrated
proteins favors the GB method. (C) 2001 Elsevier Science B.V. All rights r
eserved.