Accuracy of the three-body fragment molecular orbital method applied to Møller-Plesset perturbation theory.
The three-body energy expansion in the fragment molecular orbital method (FMO) was applied to the 2nd order Møller-Plesset theory (MP2). The accuracy of both the two and three-body expansions was determined for water clusters, alanine n-mers (alpha-helices and beta-strands) and one synthetic protein, using the 6-31G* and 6-311G* basis sets. At the best level of theory (three-body, two molecules/residues per fragment), the absolute errors in energy relative to ab initio MP2 were at most 1.2 and 5.0 mhartree, for the 6-31G* and 6-311G* basis sets, respectively. The relative accuracy was at worst 99.996% and 99.96%, for 6-31G* and 6-311G*, respectively. A three-body approximation was introduced and the optimum threshold value was determined. The protein calculation (6-31G*) at the production level (FMO2/2) took 3 h on 36 3.2-GHz Pentium 4 nodes and had the absolute error in the MP2 correlation energy of only 2 kcal/mol.
Fedorov
Dmitri G
DG
National Institute of Advanced Industrial Science and Technology, 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan.
Ishimura
Kazuya
K
Department of Theoretical Molecular Science, Institute for Molecular Science, Myodaiji, Okazaki, Aichi 444-8585, Japan.
Ishida
Toyokazu
T
National Institute of Advanced Industrial Science and Technology, 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan.
Kitaura
Kazuo
K
National Institute of Advanced Industrial Science and Technology, 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan.
Pulay
Peter
P
Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701.
Nagase
Shigeru
S
Department of Theoretical Molecular Science, Institute for Molecular Science, Myodaiji, Okazaki, Aichi 444-8585, Japan.