Second derivatives in generalized Born theory.
Generalized Born solvation models offer a popular method of including electrostatic aspects of solvation free energies within an analytical model that depends only upon atomic coordinates, charges, and dielectric radii. Here, we describe how second derivatives with respect to Cartesian coordinates can be computed in an efficient manner that can be distributed over multiple processors. This approach makes possible a variety of new methods of analysis for these implicit solvation models. We illustrate three of these methods here: the use of Newton-Raphson optimization to obtain precise minima in solution; normal mode analysis to compute solvation effects on the mechanical properties of DNA; and the calculation of configurational entropies in the MM/GBSA model. An implementation of these ideas, using the Amber generalized Born model, is available in the nucleic acid builder (NAB) code, and we present examples for proteins with up to 45,000 atoms. The code has been implemented for parallel computers using both the OpenMP and MPI environments, and good parallel scaling is seen with as many as 144 OpenMP processing threads or MPI processing tasks.
Brown
Russell A
RA
Sun Microsystems, Inc., Menlo Park, California 94025, USA.
Case
David A
DA
D000465:Algorithms; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry; D008956:Models, Chemical; D011789:Quantum Theory; D012997:Solvents / Q000737:chemistry; D055672:Static Electricity; D014732:Vibration
D012997:Solvents; D004247:DNA