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Biomedical subjects

P E Maslen

Publications and source records attributed to P E Maslen.

2 recordsLinked to original sources
PubMed2005

Geometry optimization of molecular clusters and complexes using scaled internal coordinates.

Scaled internal coordinates are introduced for use in the geometry optimization of systems composed of multiple fragments, such as solvated molecules, clusters, and biomolecular complexes. The new coordinates are related to bond lengths, bond angles and torsion angles by geometry-dependent scaling factors. The scaling factors serve to expedite the optimization of complexes containing outlying fragments, without hindering the optimization of the intramolecular degrees of freedom. Trial calculations indicate that, at asymptotic separations, the scaling factors improve the rate of convergence by a factor of 4 to 5.

Biopolymers↗
PubMed2004

Technique for incorporating the density functional Hessian into the geometry optimization of biomolecules, solvated molecules, and large floppy molecules.

Traditional geometry optimization methods require the gradient of the potential surface, together with a Hessian which is often approximated. Approximation of the Hessian causes difficulties for large, floppy molecules, increasing the number of steps required to reach the minimum. In this article, the costly evaluation of the exact Hessian is avoided by expanding the density functional to second order in both the nuclear and electronic variables, and then searching for the minimum of the quadratic functional. The quadratic search involves the simultaneous determination of both the geometry step and the associated change in the electron density matrix. Trial calculations on Taxol indicate that the cost of the quadratic search is comparable to the cost of the density functional energy plus gradient. While this procedure circumvents the bottleneck coupled-perturbed step in the evaluation of the full Hessian, the second derivatives of the electron-repulsion integrals are still required for atomic-orbital-based calculations, and they are presently more expensive than the energy plus gradient. Hence, we anticipate that the quadratic optimizer will initially find application in fields in which existing optimizers breakdown or are inefficient, particularly biochemistry and solvation chemistry.

Algorithms↗