An efficient implementation of a QM-MM method in SIESTA

Theoretical Chemistry Accounts

Volumn 128, Issue 4, 2011, Pages 825-833

  Sanz Navarro, Carlos F ^a   Grima, Rogeli ^b   García, Alberto ^c   Bea, Edgar A ^b   Soba, Alejandro ^b   Cela, J M ^b   Ordejón, Pablo ^a  

^a CATALAN INSTITUTE OF NANOSCIENCE AND NANOTECHNOLOGY ICN2   (Spain)

^b BARCELONA SUPERCOMPUTING CENTER   (Spain)

^c INSTITUT DE CIÈNCIA DE MATERIALS DE BARCELONA ICMAB CSIC   (Spain)

Author keywords

Density functional theory; Load balancing; Molecular mechanics; Parallelization

Indexed keywords

EID: 79952190966     PISSN: 1432881X     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00214-010-0816-5     Document Type: Article

References (33)

1. Zhang R, Lev B, Cuervo JE, Noskov SY, Salahub DR (2010) A guide to QM/MM methodology and applications. In: Advances in quantum chemistry, vol 59. Elsevier Accademic Press, San Diego, pp 353-400.
2. Crespo A, Scherlis DA, Martí MA, Ordejón P, Roitberg AE, Estrin DA (2003) A DFT-based QM-MM approach designed for the treatment of large molecular systems: aplication to chorismate mutase. J Phys Chem B 107: 13728-13736.
3. Soler JM, Artacho E, Gale JD, García A, Junquera J, Ordejón P, Sánchez-Portal D (2002) The Siesta method for ab initio order-N materials simulation. J Phys Condens Matter 14: 2745-2779.
4. Wang J, Cieplak P, Kollman PA (2000) How well does a restrained electrostatic potential (resp) model perform in calculating conformational energies of organic and biological molecules. J Comput Chem 21: 1049-1074.
5. Cornell WD, Cieplak P, Bayly CI, Gould IR, Merz KM Jr, Ferguson DM, Spellmeyer DC, Fox T, Caldwell JW, Kollman PA (1995) A 2nd generation force-field for the simulation of proteins, nucleic-acids, and organic-molecules. J Am Chem Soc 117: 5179-5197.
6. Scherlis DA, Martí MA, Ordejón P, Estrin DA (2002) Environment effects on chemical reactivity of heme proteins. Int J Quantum Chem 90: 1505-1514.
7. Martí MA, Scherlis DA, Doctorovich FA, Ordejón P, Estrin DA (2003) Modulation of the NO trans effect in heme proteins: implications for the activation of soluble guanylate cyclase. J Biol Inorg Chem 8: 595-600.
8. Martí MA, Capece L, Crespo A, Doctorovich F, Estrin DA (2005) Nitric oxide interaction with cytochrome c' and its relevance to guanylate cyclase. Why does the iron histidine bond break? J Am Chem Soc 127: 7721-7728.
9. Senn HM, Thiel W (2009) QM/MM methods for biomolecular systems. Angew Chem Int Ed 48: 1198-1229.
10. Eichinger M, Tavan P, Hutter J, Parrinello M (1999) A hybrid method for solutes in complex solvents: density functional theory combined with empirical force fields. J Chem Phys 110: 10452-10467.
11. Garcia A, Anglada E, Soler JM (unpublished).
12. Laino T, Mohamed FI, Laio A, Parrinello M (2006) An efficient linear-scaling electrostatic coupling for treating periodic boundary conditions in QM/MM simulations. J Chem Theory Comput 2: 1370-1378.
13. Perdew JP, Burke K, Ernzerhof M (1996) Generalized gradient approximation made simple. Phys Rev Lett 77: 3865-3868.
14. Fernández-Serra MV, Artacho E (2006) Electrons and hydrogen-bond connectivity in liquid water. Phys Rev Lett 96: 016404.
15. 2O. J Chem Phys 59: 2254-2259.
16. Wei D, Salahub DR (1994) A combined density functional and molecular dynamics simulation of a quantum water molecule in aqueous solution. Chem Phys Lett 224: 291-296.
17. The dipole obtained with Siesta using a basis set with triple-ζ plus double polarization orbitals, and cutoff radii of around 9 a. u. is 1. 86 D, very close to the experimental value of 1. 85 D.
18. Jorgensen WL (1981) Quantum and statistical mechanical studies of liquids. 10. Transferable intermolecular potential functions for water, alcohols, and ethers. Application to liquid water. J Am Chem Soc 103: 335-340.
19. Eichinger M, Tavan P, Hutter J, Parrinello M (1999) A hybrid method for solutes in complex solvents: density functional theory combined with empirical force fields. J Chem Phys 110: 10452-10467.
20. Takahashi H, Hori T, Hashimoto H, Nitta T (2001) A hybrid QM/MM method employing real space grids for QM water in the TIP4P water solvents. J Comput Chem 22: 1252-1261.
21. Tu Y, Laaksonen A (1999) On the effect of Lennard-Jones parameters on the quantum mechanical and molecular mechanics coupling in a hybrid molecular dynamics simulation of liquid water. J Chem Phys 111: 7519-7525.
22. Lofere MJ, Loeffler HH, Liedl KR (2003) A QM-MM interface between CHARMM and Turbomole: implementation and application to systems in bulk phase and biologically active systems. J Comput Chem 24: 1240-1249.
23. Tunón I, Martins-Costa MTC, Millot C, Ruiz-López MF, Rivail JL (1996) A coupled density functional-molecular mechanics monte carlo simulation method: the water molecule in liquid water. J Chem Phys 17: 19-29.
24. 2O vapors by measurement of thermal conductivity. J Chem Phys 71: 2703-2711.
25. Perdew JP, Wang Y (1992) Accurate and simple analytic representation of the electron-gas correlation energy. Phys Rev B 45: 13244-13249.
26. Biswas PK, Gogonea V (2005) A regularized and renormalized electrostatic coupling Hamiltonian for hybrid quantum-mechanical-molecular-mechanical calculations. J Phys Chem 123: 164114.
27. Lyne PD, Hodoscek M, Karplus M (1999) A hybrid QM-MM potential employing hartree-fock or density functional methods in the quantum region. J Phys Chem A 103: 3462-3471.
28. 2O molecule in ice. Proc R Soc A (Lond) 291: 445-453.
29. Pillet V, Labarta J, Cortés T, Girona S (1995) Paraver: a tool to visualize and analyze parallel code. Transputer and occam developments, pp 17-32, http://www. bsc. es/paraver.
30. MPItrace instrumentation package, http://www. bsc. es/plantillaA. php?catid=492.
31. Simon HD, Teng S (1995) How good is recursive bisection? SIAM J Sci Comput.
32. Garey MR, Johnson DS (1979) Computers and intractability: a guide to the theory of NP-completeness. W. H. Freeman, New York.
33. Welsch D, Powel MB (1967) An upper bound for the chromatic number of a graph and its application to timetabling problems. Comput J.