Chemistry, Ames Laboratory
Journal or Book Title
Journal of Chemical Physics
The Z-vector equations are derived and implemented for solving the response term due to the external electrostatic potentials, and the corresponding contribution is added to the energy gradients in the framework of the fragment molecular orbital (FMO) method. To practically solve the equations for large molecules like proteins, the equations are decoupled by taking advantage of the local nature of fragments in the FMO method and establishing the self-consistent Z-vector method. The resulting gradients are compared with numerical gradients for the test molecular systems: (H2O)64, alanine decamer, hydrated chignolin with the protein data bank (PDB) ID of 1UAO, and a Trp-cage miniprotein construct (PDB ID: 1L2Y). The computation time for calculating the response contribution is comparable to or less than that of the FMO self-consistent charge calculation. It is also shown that the energy gradients for the electrostatic dimer approximation are fully analytic, which significantly reduces the computational costs. The fully analytic FMO gradient is parallelized with an efficiency of about 98% on 32 nodes.
Copyright 2011 American Institute of Physics. This article may be downloaded for personal use only. Any other use requires prior permission of the author and the American Institute of Physics.
American Institute of Physics
Nagata, Takeshi; Brorsen, Kurt Ryan; Fedorov, Dmitri G.; Kitaura, Kazuo; and Gordon, Mark S., "Fully Analytic Energy Gradient in the Fragment Molecular Orbital Method" (2011). Ames Laboratory Publications. 345.