Journal of Grid Computing

, Volume 8, Issue 4, pp 571–586 | Cite as

COMPCHEM: Progress Towards GEMS a Grid Empowered Molecular Simulator and Beyond

  • Antonio Laganà
  • Alessandro Costantini
  • Osvaldo Gervasi
  • Noelia Faginas Lago
  • Carlo Manuali
  • Sergio Rampino


Foundations and structure of the building blocks of GEMS, the ab initio molecular simulator designed for implementation on the EGEE computing Grid, are analyzed. The impact of the computational characteristics of the codes composing its blocks (the calculation of the ab initio potential energy values, the integration of the dynamics equations of the nuclear motion, and the statistical averaging of microscopic information to evaluate the relevant observable properties) on their Grid implementation when using rigorous ab initio quantum methods are discussed. The requests prompted by this approach for new computational developments are also examined by considering the present implementation of the simulator that is specialized in atom diatom reactive exchange processes.


Grid EGEE Molecular dynamics 


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. 1.
    Laganà, A. (ed.): Supercomputer Algorithms for Reactivity, Dynamics and Kinetics of Small Molecules. Kluwer, Dordrecht. (1989). ISBN 0-7923-0226-5Google Scholar
  2. 2.
    Hirst, D.M.: A Computational Approach to Chemistry. Blackwell Scientific Publications, Oxford (1990). ISBN 0-632-02431-3Google Scholar
  3. 3.
    Schatz, G.C., Ratner, M.A.: Quantum Mechanics in Chemistry. Prentice Hall, Englewood Cliffs (1993). ISBN 0-13-075011-5Google Scholar
  4. 4.
    Laganà, A., Riganelli, A. (eds.): Lecture Notes in Chemistry. Springer, Berlin (2000). ISBN 3-540-41202-6Google Scholar
  5. 5.
    Laganà, A., Lendvay, G. (eds.): Theory of Chemical Reaction Dynamics. Kluwer, Dordrecht (2004). ISBN 1-4020-2165-6Google Scholar
  6. 6.
    Laganà, A., Riganelli, A.: Computational Reaction and Molecular Dynamics: From Simple Systems and Rigorous Methods to Complex Systems and Approximate Methods. Lecture Notes in Chemistry, vol. 75, 1–10 (2000)Google Scholar
  7. 7.
    Gervasi, O., Crocchianti, S., Pacifici, L., Skouteris, D., Laganà, A.: Towards the Grid design of the dynamics engine of a molecular simulator. In: Lecture Series in Computer and Computational Science, vol. 7, pp. 1425–1428 (2006)Google Scholar
  8. 8.
    Gervasi, O., Manuali, C., Laganà, A., Costantini, A.: On the structuring of a molecular simulator as a Grid service. In: Chemistry and Material Science Applications on Grid Infrastructures. ICTP Lecture Notes, vol. 24, pp. 63–82 (2009). ISBN 92-95003-42-XGoogle Scholar
  9. 9.
    Laganà, A., Riganelli, A., Gervasi, O.: On the structuring of the computational chemistry virtual organization COMPCHEM. Lect. Notes Comput. Sci. 3980, 665–674 (2006). CrossRefGoogle Scholar
  10. 10.
    EGEE (Enabling Grids for E-Science in Europe):
  11. 11.
    Gervasi, O., Laganà, A.: SIMBEX: a portal for the a priori simulation of crossed beam experiments. Future Gener. Comput. Syst. 20(5), 703–716 (2004)CrossRefGoogle Scholar
  12. 12.
  13. 13.
    Costantini, A.: Computational chemistry—requirements and experiences with use of MPI. In: EGEE, EGEE’09, Barcelona, September 09.
  14. 14.
    Costantini, A., Laganà, A., Gervasi, O.: Multiscale Study of O3 Tropospheric in Middle Italy.
  15. 15.
    Chapman, S., Gelb, A., Bunker, D.L.: A + BC: A General Triatomic Classical Trajectory Program. Quantum Chemistry Program Exchange, QCPE 273, Indiana University (1975)Google Scholar
  16. 16.
    Polanyi, J.C., Schreiber, J.L.: The dynamics of bimolcular reactions in physical chemistry. An advanced treatise. In: Eyring, H., Jost, W., Henderson, D. (eds.) Kinetics of Gas Reactions, vol. VI, p. 383. Academic, New York (1974)Google Scholar
  17. 17.
    Storchi, L., Tarantelli, F., Laganà, A.: Computing molecular energy surfaces on a Grid. Lect. Notes Comput. Sci. 3980, 675–683 (2006)CrossRefGoogle Scholar
  18. 18.
    Verdicchio, M.: Thesis of the Euromaster in Theoretical Chemistry and Computational Modelling, Perugia (2009)Google Scholar
  19. 19.
    Gordon, M.S., Schmidt, M.W.: Advances in electronic structure theory: GAMESS a decade later. In: Dykstra, C.E., Frenking, G., Kim, K.S., Scuseria, G.E. (eds.) Theory and Applications of Computational Chemistry: The First Forty Years, pp. 1167–1189. Elsevier, Amsterdam (2005)CrossRefGoogle Scholar
  20. 20.
    DALTON: A Molecular Electronic Structure Program, Release 2.0 (2005). See
  21. 21.
    Werner, H.J., Knowles, P.J.: MOLPRO: A Package of Ab Initio Programs, Version 2002.6.
  22. 22.
    Frisch, M.J., Trucks, G.W., Schlegel, H.B., Scuseria, G.E., Robb, M.A., Cheeseman, J.R., Scalmani, G., Barone, V., Mennucci, B., Petersson, G.A., Nakatsuji, H., Caricato, M., Li, X., Hratchian, H.P., Izmaylov, A.F., Bloino, J., Zheng, G., Sonnenberg, J.L., Hada, M., Ehara, M., Toyota, K., Fukuda, R., Hasegawa, J., Ishida, M., Nakajima, T., Honda, Y., Kitao, O., Nakai, H., Vreven, T., Montgomery, Jr., J.A., Peralta, J.E., Ogliaro, F., Bearpark, M., Heyd, J.J., Brothers, E., Kudin, K.N., Staroverov, V.N., Kobayashi, R., Normand, J., Raghavachari, K., Rendell, A., Burant, J.C. Iyengar, S.S. Tomasi, J. Cossi, M. Rega, Millam, N.J., Klene, M. Knox, J.E., Cross, J.B., Bakken, V., Adamo, C., Jaramillo, J., Gomperts, R.E., Stratmann, O., Yazyev, A.J., Austin, R., Cammi, C., Pomelli, J.W., Ochterski, R., Martin, R.L., Morokuma, K., Zakrzewski, V.G., Voth, G.A., Salvador, P., Dannenberg, J.J., Dapprich, S., Daniels, A.D., Farkas, O., Foresman, J.B., Ortiz, J.V., Cioslowski, J., Fox, D.J.: Gaussian 09, Revision A.1. Gaussian, Wallingford (2009)Google Scholar
  23. 23.
    Arteconi, L., Laganà, A., Pacifici, L.: A web based application to fit potential energy functionals to ab initio values. Lect. Notes Comput. Sci. 3980, 694–700 (2006)CrossRefGoogle Scholar
  24. 24.
    Angeli, C., Bendazzoli, G.L., Borini, S., Cimiraglia, R., Emeerson, A., Evangelisti, S., Maynau, D., Monari, A., Rossi, E., Sanchez-Marin, J., Szalay, P.G., Tajti, A.: The problem of interoperability: a common data format for quantum chemistry codes. Int. J. Quant. Chem. 107, 2082–2091 (2007)CrossRefGoogle Scholar
  25. 25.
    Schatz, G.C.: Potential energy surfaces. Lect. Notes Chem. 75, 15–32 (2000)Google Scholar
  26. 26.
    Murrell, J.N., Carter, S., Farantos, S.C., Huxley, P., Varandas, A.J.C.: Molecular Potential Energy Functions. Wiley, London (1984)Google Scholar
  27. 27.
    Garcia, E., Laganà, A.: Diatomic potential functions for triatomic scattering. Mol. Phys. 56, 621–627 (1985)CrossRefGoogle Scholar
  28. 28.
    Garcia, E., Laganà, A.: A new bond order functional form for triatomic molecules: a fit of the BeFH potential energy. Mol. Phys. 56, 629–639 (1985)CrossRefGoogle Scholar
  29. 29.
    Aguado, A., Tablero, C., Paniagua, M.: Global fit of ab initio potential energy surfaces I: triatomic systems. Comput. Phys. Commun. 108, 259–266 (1998)zbMATHCrossRefGoogle Scholar
  30. 30.
    Laganà, A.: A rotating bond order formulation of the atom diatom potential energy surface. J. Chem. Phys. 95, 2216–2217 (1991)CrossRefGoogle Scholar
  31. 31.
    Laganà, A., Ochoa de Aspuru, G., Garcia, E.: The largest angle generalization of the rotating bond order potential: three different atom reactions. J. Chem. Phys. 108, 3886–3896 (1998)CrossRefGoogle Scholar
  32. 32.
    Rodriguez, A., Garcia, E., Hernandez, M.L., Laganà, A.: A LAGROBO strategy to fit potential energy surfaces: the OH + HCl reaction. Chem. Phys. Lett. 360, 304–312 (2002)CrossRefGoogle Scholar
  33. 33.
    Skouteris, D., Pacifici, L., Laganà, A.: Time dependent wavepacket calculations for the N(4S) + N2(\(^1\Sigma^+_g\)) system on a LEPS surface: inelastic and reactive probabilities. Mol. Phys. 102(21–22), 2237–2248 (2004)CrossRefGoogle Scholar
  34. 34.
    Pack, R.T.: Space-fixed vs body-fixed axes in atom-diatomic molecule scattering. Sudden approximations. J. Chem. Phys. 60, 633–700 (1974)CrossRefGoogle Scholar
  35. 35.
    McGuire, P.M., Kouri, D.: Quantum mechanical close coupling approach to molecular collisions: jz-conserving coupled states approximation. J. Chem. Phys. 60 2488–2503 (1974)CrossRefGoogle Scholar
  36. 36.
    Balint-Kurti, G.G.: Time dependent quantum approaches to chemical reactivity. Lect. Notes Chem. 75, 74–87 (2000)Google Scholar
  37. 37.
    Garcia, E., Saracibar, A., Laganà, A., Balucani, N.: On the anomaly of the quasiclassical product distributions of the OH + CO → H + CO2 reaction. Theor. Chem. Acc. (in press)Google Scholar
  38. 38.
    Tsai, Y.R., Cheng, L.T., Osher, S., Zhao, H.K.: Fast sweeping algorithms for a cLass of Hamilton–Jacobi equations. SIAM J. Numer. Anal. 41, 673–694 (2003)zbMATHCrossRefMathSciNetGoogle Scholar
  39. 39.
    Skouteris, D., Castillo, J.F., Manolopulos, D.E.: ABC: a quantum reactive scatering program. Comput. Phys. Commun. 133, 128–135 (2000)zbMATHCrossRefGoogle Scholar
  40. 40.
    Schatz, G.C.: Quantum reactive scattering using hyperspherical coordinates: results for H + H2 and Cl + HCl. Chem. Phys. Lett. 150, 92–98 (1998)CrossRefGoogle Scholar
  41. 41.
    Casavecchia, P., Balucani, N., Volpi, G.G.: The chemical dynamics and kinetics of small radicals. In: Lin, K., Wagner, A.F. (eds.) Adv. Ser. Phys. Chem., vol. 6, chapter 9. World Scientific, Singapore (1995)Google Scholar
  42. 42.
    Lee, Y.T.: In: Scoles, G. (ed.) Atomic and Molecular Beam Method. Oxford University Press, New York (1987)Google Scholar
  43. 43.
    Siska, P.E.: Iterative unfolding of intensity data, with application to molecular beam scattering. J. Chem. Phys. 59, 6052 (1973)CrossRefGoogle Scholar
  44. 44.
    Skouteris, D., De Fazio, D., Cavalli, S., Aquilanti, V.: Quantum stereodynamics for the two product channels of the F + HD reaction from the complete scattering matrix in the stereodirected representation. J. Phys. Chem. A 113, 14807–14812 (2009)CrossRefGoogle Scholar
  45. 45.
    Saracibar, A., Sanchez, C., Garcia, E., Laganà, A., Skouteris, D.: Grid computing in time dependent quantum reactive dynamics. Lect. Notes Comput. Sci. 5072, 1065–1080 (2008)CrossRefGoogle Scholar
  46. 46.
    Bellucci, D., Tasso, S., Laganà, A.: Parallel model for a discrete variable wavepacket propagation. Lect. Notes Comput. Sci. 2658, 341–349 (2003)CrossRefGoogle Scholar
  47. 47.
    Gregori, S., Tasso, S., Laganà, A.: Fine grain parallelization of a discrete variable wavepacket calculation using ASSIST-CL. Lect. Notes Comput. Sci. 3044, 437–444 (2004)CrossRefGoogle Scholar
  48. 48.
    Kacsuk, P., Sipos, G.: Multi-Grid, Multi-user workflows in the P-GRADE portal. Journal of Grid Computing 3(3–4), 221–238 (2005)CrossRefGoogle Scholar
  49. 49.
    Kacsuk, P., Dózsa, G., Kovács, J., Lovas, R., Podhorszki, N.Z., Balaton Gombás, G.: P-GRADE: a Grid programming environment. Journal of Grid Computing 1. 171–197 (2003)CrossRefGoogle Scholar
  50. 50.
    Kacsuk, P., Farkas, Z., Herman, G.: Workflow-level parameter study support for production Grids. Lect. Notes in Comput. Sci. 4707, 872–885 (2007)CrossRefGoogle Scholar
  51. 51.
    Skouteris, D., Costantini, A., Laganà, A., Sipos, G., Balaski, A., Kacsuk, P.: Implementation of the ABC quantum mechanical reactive scattering program on the EGEE Grid platform. Lect. Notes Comput. Sci. 5072, 1108–1120 (2008)CrossRefGoogle Scholar
  52. 52.
    Multi-Grid installation of P-GRADE portal:
  53. 53.
    Kacsuk, P., Sipos, G.: Multi-Grid, Multi-user workflows in the P-GRADE Grid portal. Journal of Grid Computing 3, 221–238 (2006)CrossRefGoogle Scholar
  54. 54.
    Rampino, S., Skouteris, D., Laganà, A., Garcia, E.: A comparison of the isotope effect for the N + N2reaction calculated on two potential energy surfaces. Lect. Notes Comput. Sci. 5072, 1081–1093 (2008)CrossRefGoogle Scholar
  55. 55.
    Rampino, S., Skouteris, D., Laganà, A.: The O + O2 reaction: quantum detailed probabilities and thermal rate coefficients. Theor. Chem. Acc. 123, 249–256 (2009)CrossRefGoogle Scholar
  56. 56.
    Manolopulos, D.E.: An improved log derivative method for inelastic scattering. J. Chem. Phys. 85, 6425–6429 (1986)CrossRefGoogle Scholar
  57. 57.
    Pack, R.T., Parker, G.A.: Quantum scattering in the three dimentions using hyperspherical (APH) coordinates. Theory. J. Chem. Phys. 87, 3888–3921 (1987)Google Scholar
  58. 58.
    Manuali, C., Laganà, A., Rampino, S.: GRIF: a Grid Framework for a web service approach to reactive scattering. Comp. Phys. Commun. 181, 1179–1185 (2010)CrossRefGoogle Scholar
  59. 59.
  60. 60.

Copyright information

© Springer Science+Business Media B.V. 2010

Authors and Affiliations

  • Antonio Laganà
    • 1
  • Alessandro Costantini
    • 2
  • Osvaldo Gervasi
    • 2
  • Noelia Faginas Lago
    • 1
  • Carlo Manuali
    • 2
  • Sergio Rampino
    • 1
  1. 1.Department of ChemistryUniversity of PerugiaPerugiaItaly
  2. 2.Department of Mathematics and InformaticsUniversity of PerugiaPerugiaItaly

Personalised recommendations