Fragment molecular orbital
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The fragment molecular orbital method (FMO) is a computational method that can compute very large molecular systems with thousands of atoms using ab initio quantum-chemical wave functions.
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[edit] Introduction
The fragment molecular orbital method (FMO) was proposed by K. Kitaura and coworkers in 1999. FMO is deeply interconnected with the well known energy decomposition analysis (EDA) by Kitaura and Morokuma, developed in 1976. The main use of FMO is to compute very large molecular systems by dividing them into fragments and performing ab initio quantum-mechanical calculations of fragments and their dimers, whereby the Coulomb field from the whole system is included. The latter feature allows fragment calculations without unphysical caps and results in the proper electron density treatment of the whole system.
In addition to the calculation of the total properties, such as the energy, energy gradient, dipole moment etc, the pair interaction is obtained for each pair of fragments. This pair interaction energy can be further decomposed into electrostatic, exchange, charge transfer and dispersion contributions. This analysis is known as the pair interaction energy decomposition analysis (PIEDA) and it can be thought of as FMO-based EDA.
The rapid development of the FMO method made possible to use common wave functions for ab initio calculations of fragments and their dimers, such as Hartree-Fock, Density functional theory (DFT), Multi-configurational self-consistent field (MCSCF), time-dependent DFT (TDDFT), configuration interaction (CI), second order Møller-Plesset perturbation theory (MP2), and coupled cluster (CC).
The solvent effects can be treated with the polarizable continuum model (PCM). The FMO code is very efficiently parallelized utilising the generalized distributed data interface (GDDI) and hundreds of CPUs can be used with nearly perfect scaling.
Since very large systems can be computed with high level ab initio wave functions, FMO is thought to be very useful for biological applications to compute the whole proteins and their complexes. In 2005, an application of FMO to the calculation of the ground electronic state of photosynthetic protein with more than 20,000 atoms was distinguished with the best technical paper award at Supercomputing 2005. A number of applications of FMO to biochemical problems have been published [1]. In particular, the FMO method is a promising tool for drug design as well as the studies of excitated states and chemical reactions of biological systems
The FMO method is implemented in GAMESS (US) and ABINIT-MP software pacakages. Both are distributed free of charge. The preparation of the input files is facilitated with the FMOutil software availale at http://staff.aist.go.jp/d.g.fedorov/fmo/fmoutil.html].
[edit] See also
[edit] References
- K. Kitaura et al. (1999). "Fragment molecular orbital method: an approximate computational method for large molecules". Chem. Phys. Lett. 313: 701–706. doi:.
- D. G. Fedorov, K. Kitaura, Theoretical development of the fragment molecular orbital (FMO) method, in Modern methods for theoretical physical chemistry of biopolymers, edited by E. Starikov, J. Lewis, S. Tanaka, Elsevier, Amsterdam, 2006.
- D. G. Fedorov et al. (2007). "Extending the Power of Quantum Chemistry to Large Systems with the Fragment Molecular Orbital Method". J. Phys. Chem. A 111: 6904–6914. doi:.
