title: Fully analytic energy gradient in the fragment molecular orbital method.
abstract: 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: (H(2)O)(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.
authors: NRI, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan. takeshi.nagata@aist.go.jp
authors: Takeshi
authors: T
authors: Nagata
authors: Kurt
authors: K
authors: Brorsen
authors: Dmitri G
authors: DG
authors: Fedorov
authors: Kazuo
authors: K
authors: Kitaura
authors: Mark S
authors: MS
authors: Gordon
mesh_terms: D000409:Alanine / Q000031:analogs & derivatives; D056004:Molecular Dynamics Simulation; D009842:Oligopeptides / Q000737:chemistry; D011506:Proteins / Q000737:chemistry*; D011789:Quantum Theory
chemical_list: D009842:Oligopeptides; D011506:Proteins; C506175:chignolin; D000409:Alanine