Three-body expansion and generalized dynamic fragmentation improve the fragment molecular orbital-based molecular dynamics (FMO-MD)☆

Abstract The fragment molecular orbital-based molecular dynamics (FMO-MD) was improved by the introduction of the three-body extension (FMO3) and the generalized dynamic fragmentation. An analytical energy gradient was derived for FMO3 to realize FMO3-MD. An algorithm of generalized dynamic fragmentation was devised to treat each covalent-bonded and, optionally, hydrogen-bonded atom cluster as a fragment in the course of FMO-MD. The new algorithms were tested by performing conventional MO-MD, FMO2-MD, based on two-body extension, and FMO3-MD simulations of (H 2 O) 32 and H + (H 2 O) 32 . FMO2-MD resulted in lower precision, especially in H + (H 2 O) 32 , while FMO3-MD gave a precision comparable to that of MO-MD.

[1]  Kazuo Kitaura,et al.  The three-body fragment molecular orbital method for accurate calculations of large systems , 2006 .

[2]  S. Iwata.  Absolutely local excited orbitals in the higher order perturbation expansion for the molecular interaction. , 2008, The journal of physical chemistry. B.

[3]  K. Kitaura,et al.  Fragment molecular orbital method: an approximate computational method for large molecules , 1999 .

[4]  Kaori Fukuzawa,et al.  Large scale FMO-MP2 calculations on a massively parallel-vector computer , 2008 .

[5]  Yuto Komeiji,et al.  Fragment molecular orbital-based molecular dynamics (FMO-MD), a quantum simulation tool for large molecular systems , 2009 .

[6]  S. Harvey,et al.  The flying ice cube: Velocity rescaling in molecular dynamics leads to violation of energy equipartition , 1998, J. Comput. Chem..

[7]  Æleen Frisch,et al.  Exploring chemistry with electronic structure methods , 1996 .

[8]  M. Gordon,et al.  A combined effective fragment potential-fragment molecular orbital method. I. The energy expression and initial applications. , 2009, The Journal of chemical physics.

[9]  Kaori Fukuzawa,et al.  Accuracy of fragmentation in ab initio calculations of hydrated sodium cation , 2009 .

[10]  K. Jordan,et al.  Theoretical study of the n-body interaction energies of the ring, cage and prism forms of (H2O)6 , 1998 .

[11]  M J Elrod,et al.  Many-body effects in intermolecular forces. , 1994, Chemical reviews.

[12]  Makoto Taiji,et al.  Fast and accurate molecular dynamics simulation of a protein using a special‐purpose computer , 1997 .

[13]  Yuichi Inadomi,et al.  Fragment molecular orbital method: application to molecular dynamics simulation, ‘ab initio FMO-MD’ , 2003 .

[14]  Kazuo Kitaura,et al.  The Fragment Molecular Orbital Method: Practical Applications to Large Molecular Systems , 2009 .

[15]  Takeshi Ishikawa,et al.  A fully quantum mechanical simulation study on the lowest n-π* state of hydrated formaldehyde , 2007 .

[16]  Yuto Komeiji,et al.  Fragment molecular orbital method: analytical energy gradients , 2001 .

[17]  Takeshi Ishikawa,et al.  Fragment Molecular Orbital method‐based Molecular Dynamics (FMO‐MD) as a simulator for chemical reactions in explicit solvation , 2009, J. Comput. Chem..

[18]  Kazuo Kitaura,et al.  Derivatives of the approximated electrostatic potentials in the fragment molecular orbital method , 2009 .

[19]  Kaori Fukuzawa,et al.  Fragment molecular orbital method: use of approximate electrostatic potential , 2002 .

[20]  Yuichi Inadomi,et al.  PEACH 4 with ABINIT-MP: a general platform for classical and quantum simulations of biological molecules. , 2004, Computational biology and chemistry.

[21]  Marat Valiev,et al.  Fast electron correlation methods for molecular clusters without basis set superposition errors. , 2008, The Journal of chemical physics.

[22]  Masami Uebayasi,et al.  The fragment molecular orbital method for geometry optimizations of polypeptides and proteins. , 2007, The journal of physical chemistry. A.

[23]  Makoto Haraguchi,et al.  Parallel molecular dynamics simulation of a protein , 2001, Parallel Comput..

[24]  Yutaka Akiyama,et al.  Fragment molecular orbital method: application to polypeptides , 2000 .

[25]  Mark S. Gordon,et al.  A new hierarchical parallelization scheme: Generalized distributed data interface (GDDI), and an application to the fragment molecular orbital method (FMO) , 2004, J. Comput. Chem..

[26]  M. Klein,et al.  Nosé-Hoover chains : the canonical ensemble via continuous dynamics , 1992 .

[27]  J. M. Haile,et al.  Molecular dynamics simulation : elementary methods / J.M. Haile , 1992 .

[28]  Shridhar R Gadre,et al.  Many-body interaction analysis: algorithm development and application to large molecular clusters. , 2004, The Journal of chemical physics.

[29]  Takeshi Ishikawa,et al.  How does an S(N)2 reaction take place in solution? Full ab initio MD simulations for the hydrolysis of the methyl diazonium ion. , 2008, Journal of the American Chemical Society.

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