Systematic study of the embedding potential description in the fragment molecular orbital method.
We analyzed the accuracy of the fragment molecular orbital method using various representations of the embedding potential and extended its applicability to large basis sets by proposing to use potential-derived point charges with screening combined with the adaptive frozen orbital treatment of the detached bonds. A comprehensive set of basis sets: STO-3G, 6-31G*, 6-311G*, 6-31++G**, 6-311++G**, cc-pVDZ, cc-pVTZ, aug-cc-pVDZ, and aug-cc-pVTZ was employed; for tests systems we used water clusters with 16 and 32 molecules, the alpha-helices and beta-strands of alanine containing 10 and 20 residues, as well as chignolin (PDB: 1UAO ) and Trp-cage miniprotein (PDB: 1L2Y ).
Fedorov
Dmitri G
DG
Research Institute for Computational Sciences (RICS), National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan. d.g.fedorov@aist.go.jp
Slipchenko
Lyudmila V
LV
Kitaura
Kazuo
K
D056004:Molecular Dynamics Simulation; D011789:Quantum Theory