A fragment energy assembler method for Hartree-Fock calculations of large molecules.

We present a fragment energy assembler approach for approximate Hartree-Fock (HF) calculations of macromolecules. In this method, a macromolecule is divided into small fragments with appropriate size, and then each fragment is capped by its neighboring fragments to form a subsystem. The total energy of the target system is evaluated as the sum of the fragment energies of all fragments, which are available from conventional HF calculations on all subsystems. By applying the method to a broad range of molecules, we demonstrate that the present approach could yield satisfactory HF energies for all studied systems.

[1]  Robert Wieczorek,et al.  Comparison of fully optimized alpha- and 3(10)-helices with extended beta-strands. An ONIOM density functional theory study. , 2004, Journal of the American Chemical Society.

[2]  Gustavo E. Scuseria,et al.  What is the Best Alternative to Diagonalization of the Hamiltonian in Large Scale Semiempirical Calculations , 1999 .

[3]  Kazuo Kitaura,et al.  The importance of three-body terms in the fragment molecular orbital method. , 2004, The Journal of chemical physics.

[4]  J. Kinoshita.  Simple Life Satisfies This Grad Student , 1996, Science.

[5]  D. York,et al.  Linear‐scaling semiempirical quantum calculations for macromolecules , 1996 .

[6]  Wei Li,et al.  An efficient fragment-based approach for predicting the ground-state energies and structures of large molecules. , 2005, Journal of the American Chemical Society.

[7]  Mark S. Gordon,et al.  General atomic and molecular electronic structure system , 1993, J. Comput. Chem..

[8]  Yang,et al.  Direct calculation of electron density in density-functional theory. , 1991, Physical review letters.

[9]  Benny G. Johnson,et al.  Linear scaling density functional calculations via the continuous fast multipole method , 1996 .

[10]  Clemens C. J. Roothaan,et al.  New Developments in Molecular Orbital Theory , 1951 .

[11]  Paul G. Mezey,et al.  Ab initio quality properties for macromolecules using the ADMA approach , 2003, J. Comput. Chem..

[12]  Kazuo Kitaura,et al.  On the accuracy of the 3-body fragment molecular orbital method (FMO) applied to density functional theory , 2004 .

[13]  István Mayer,et al.  A chemical energy component analysis , 2000 .

[14]  P. Salvador,et al.  Density functional energy decomposition into one- and two-atom contributions. , 2005, The Journal of chemical physics.

[15]  István Mayer,et al.  An exact chemical decomposition scheme for the molecular energy , 2003 .

[16]  Xiao He,et al.  A new method for direct calculation of total energy of protein. , 2005, The Journal of chemical physics.

[17]  Gustavo E. Scuseria,et al.  Linear Scaling Density Functional Calculations with Gaussian Orbitals , 1999 .

[18]  Martin Head-Gordon,et al.  Derivation and efficient implementation of the fast multipole method , 1994 .

[19]  Michael A Collins,et al.  Approximate ab initio energies by systematic molecular fragmentation. , 2005, The Journal of chemical physics.

[20]  Weitao Yang,et al.  A density‐matrix divide‐and‐conquer approach for electronic structure calculations of large molecules , 1995 .

[21]  Enrico Clementi,et al.  Study of the Electronic Structure of Molecules. I. Molecular Wavefunctions and Their Analysis , 1967 .

[22]  K. Merz,et al.  Implementation and Testing of a Frozen Density Matrix−Divide and Conquer Algorithm , 1999 .

[23]  John Z H Zhang,et al.  An efficient approach for ab initio energy calculation of biopolymers. , 2005, The Journal of chemical physics.

[24]  Hiromi Nakai,et al.  Energy density analysis with Kohn-Sham orbitals , 2002 .

[25]  Paul G. Mezey,et al.  The Field-Adapted ADMA Approach: Introducing Point Charges , 2004 .

[26]  Michael J. Frisch,et al.  Improving harmonic vibrational frequencies calculations in density functional theory , 1997 .

[27]  Eric Schwegler,et al.  Linear scaling computation of the Hartree–Fock exchange matrix , 1996 .

[28]  S. L. Dixon,et al.  Semiempirical molecular orbital calculations with linear system size scaling , 1996 .

[29]  Christian Ochsenfeld,et al.  Linear and sublinear scaling formation of Hartree-Fock-type exchange matrices , 1998 .

[30]  Gustavo E. Scuseria,et al.  Linear scaling conjugate gradient density matrix search as an alternative to diagonalization for first principles electronic structure calculations , 1997 .

[31]  G. Scuseria,et al.  Atom pair partitioning of the correlation energy , 2000 .

[32]  Gustavo E. Scuseria,et al.  A quantitative study of the scaling properties of the Hartree–Fock method , 1995 .

[33]  Wei Li,et al.  A localized molecular-orbital assembler approach for Hartree-Fock calculations of large molecules. , 2005, The Journal of chemical physics.

[34]  Michael J. Frisch,et al.  Achieving linear scaling in exchange-correlation density functional quadratures , 1996 .

[35]  S. L. Dixon,et al.  Fast, accurate semiempirical molecular orbital calculations for macromolecules , 1997 .

[36]  Michael J. Frisch,et al.  Density matrix search using direct inversion in the iterative subspace as a linear scaling alternative to diagonalization in electronic structure calculations , 2003 .