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Grid based Molecular Simulators

This document provides a summary of the first meeting of the COST Chemistry and METACHEM advisory panel, which took place on June 14th, 2004, at CERN, Geneva. It includes information on ongoing metalaboratories in Chemistry and the architecture of the simulator. The participation of non-COST institutions in the meeting is also listed.

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Grid based Molecular Simulators

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  1. EGEE Generic Applications Advisory Panelfirst meeting Grid based Molecular Simulators CERN, Geneva, June 14th, 2004 Osvaldo Gervasi Dept. of Mathematics and Computer Science University of Perugia ogervasi@computer.org Antonio Laganà Dept. of Chemistry University of Perugia lag@dyn.unipg.it

  2. Summary • COST Chemistry and METACHEM • Ongoing metalaboratories in Chemistry • Architecture of the Simulator • Conclusions

  3. Participation of Non-COST Institutions (Total: 78) • Ukraine (8) • USA (16) • Russia (22) • Algeria (1) • Armenia (2) • Argentina (1) • Australia (3) • NGO (3) • Canada (13) • Japan (6) • China (2) • India (1) • Eritrea (1) COST- Countries (2002) Participating Institutions • EU COST States (2078) • Turkey (20) • Non COST (78) • Switzerland (143) • Israel (27) • EU Framework Programme • FYROM (4) associated states (902) • F.R.Y. (6) • Austria (152) • Slovenia (100) • Belgium (165) • Other COST States (211) • Croatia (38) • Denmark (133) • Slovakia (48) • Cooperating States (27) • Romania (67) • Finland (137) • Poland (105) • Participation of non-COST institutions (Details on following Chart) • Norway (124) • France (174) • Malta (12) • Lithuania (42) • Germany (179) • Latvia (37) • Iceland (18) • Greece (113) • Hungary (134) • Ireland (102) • Estonia (10) • Czech Republic (104) • Italy (173) • Cyprus (52) • Luxembourg (6) • Bulgaria (49) • Netherlands (150) • Spain (184) • United Kingdom (180) • Portugal (96) • Sweden (134)

  4. COST Member States • The twentyfive EU Member States • EFTA Member States • Iceland • Norway • Switzerland* • Candidate Counties • Bulgaria • Romania • Turkey * • Other Countries • Federal Republic of Yugoslavia* • Former Yugoslav Republic of Macedonia* • Croatia * • Co-operating State • Israel * Not Associated to FP

  5. The COST Chemistry domain • Created in 1992 • 34 Actions launched since 1992 (12 completed with final evaluation) • 22 running (10 had the mid term evaluation) • Research Chemists from 31 COST Countries • Associated Institutions from Australia, Japan, Russia, Ukraine and the USA

  6. Second batch of Actions • Health and Therapy - D13 (New Molecules for Human Health), - D18 (Lanthanide Chemistry for Diagnosis and Therapy), - D20 (Metal Compounds in the Treatment of Cancer and Viral Diseases) • Biology and Prebiotic - D21 (Metalloenzymes and Chemical Biomimethics), - D22 (Protein Lipid Interaction), - D27 (Prebiotic Chemistry and Early Evolution), - D28 (Natural Products as a Source for Discovery, Synthesis and Application of Pharmaceuticals)

  7. Second batch of Actions • Nanostructures and new Functions and Materials - D14 (Functional Molecular Material), - D17 (Oligomers, Polymers and Copolymers via Metal Catalysis), - D31 (Organising Non-Covalent Chemical Systems with Selected Functions), - D34 (Nanoscale Electrochemical and Bioprocesses at solid aqueous interfaces of industrial materials) • New Molecules and Clean Processes - D15 (Interfacial Chemistry and Catalysis), - D24 (Sustainable Chemical Processes Stereoselective Transition Metal Catalysed Reactions), - D25 (Applied Biocatalysis: Stereoselective and Environmentally Friendly Reactions catalysed by Enzymes) - D29 (Sustainable Chemical Processes: Stereoselective Transition Metal-Catalysed Reactions)

  8. Second batch of Actions • High Pressure and Energy - D30 (High Pressure Tuning of Chemical and Biochemical Processes), - D32 (Chemistry in High Energy Microenvironments) • Theory and computing - D16 (Combinatorial Chemistry), - D23 (Metachem: Metalaboratories for Complex Computational Applications in Chemistry), - D26 (Integrative Computational Chemistry)

  9. Metachem: Matalaboratories for Complex Applications in Chemistry • MURQM: Multireference Quantum Chemical Methods • DIRAC: Four Component Relativistic Quantum Chemical Calculations • SIMBEX: Simulation of Molecular Beam Experiments • DYSTS: Dynamics and Spectroscopy of Systems : Relevant to Environment and Applied Chemistry • ELCHEM: E-learning Technologies for Chemistry • ICAB: Integration of Codes for Ab Initio Methods • COMOVIT: Collaborative Molecular and Electronic Structure Visualization tools

  10. EU partners of D23 WGs Simbex Murqm Dirac Elchem Icab Dysts Comovit

  11. Labs per nationality 1 Isr,Pl,Sk,Nl 2 Cz,Ch, Fr, Dk, A, Sw, No 3 Hu 4 Gr 5 E 6 D, Uk, 9 I

  12. MURQM (P. CARSKY, CZ) • Ab initio codes are designed in a cooperative way. They deal with large matrices and linear algebra operations. Diagonalizations and minimizations. Construction of hypersurfaces of potential energy values bypoints • 9 Laboratories (Petr Cársky - J. Heyrovsky Institute - Czech Republic, Jiri Pittner - J. Heyrovsky Institute - Czech Republic, Ivan Hubac - Comenius University – Slovakia, Stephen Wilson - Rutherford Appleton Laboratory –UK, Wolfgang Wenzel Universität Dortmund, Germany, Leszek Meissner - Nicholas Copernicus University – Poland, Volker Staemmler - Ruhr Universität – Germany, Constantinos Tsipis - Aristotle University of Thessaloniki – Greece, Aristides Mavridis - National and Kapodistrian Univ. of Athens - Greece)

  13. DIRAC (K. FAEGRI, NO) • Cooperative development of MC-SCF, gradient minimization, DFT capabilities, integral algorithms for relativistic accurate concurrent calculations • 6 Laboratories (Knut Faegri - University of Oslo – Norway, Hans J. Aagaard Jensen University of Southern Denmark – Denmark, Uzi Kaldor -Tel Aviv University – Israel, Patrick Norman - Linköping University – Sweden, Trond Saue - Université Louis Pasteur – France, Lucas Visscher - Vrije Universiteit Amsterdam – Netherlands, Timo FleigHeinrich - Heine University - Germany)

  14. SIMBEX (O. GERVASI, I) • Coordinated implementation of a workflow management environment to simulate molecular beam experiments and molecular processes. Ab initio, dynamics, kinetics and statistics codes are assembled • 10 Laboratories (Osvaldo Gervasi - Università di Perugia – Italy, Ernesto Garcia - Universidad del Pais Vasco – Spain, Gabriel Balint-Kurti - University of Bristol – UK, Gunnar Nyman - University of Goteborg – Sweden, Peter Kacsuk - MTA SZTAKI – Hungary, Jaroslaw Nabrzyski Inst. Bioorganic Chem., Poland, Francisco Tirado - Universidad Complutense – Spain, Ranieri Baraglia – CNR – Italy, Robert J. Allan – Daresbury Laboratory – UK, Gyorgy Lendvay – HAS -Hungary)

  15. DYSTS (A. AGUILAR, E) • Environment and application driven dynamics and spectroscopy calculations distributed among the participating laboratories • 4 Laboratories (Antonio Aguilar-Navarro - Universidad de Barcelona – Spain, Vincenzo Aquilanti - Università di Perugia – Italy, Florent Xavier Gadea - Université Paul Sabatier – France, Paolo Palmieri - Universita di Bologna - Italy)

  16. ELCHEM (A. LAGANA, I) • Coordinated development of ubiquitous learning technologies and virtual laboratories. Design of distributed virtual reality tools at human and molecular level • 10 Laboratories (Antonio Laganà - Università di Perugia – Italy, Ernst Bratz - TU Muenchen – Germany, Gustavo Avitabile - Università Federico II – Italy, Dimitra Kovala-Demertzi - University of Ioannina – Greece, Jens Josephsen - Roskilde University – Denmark, Paul Yates - Keele University – UK, Anna Croft - University of Wales – UK, Evangelia Varella - University of Thessaloniki – Greece)

  17. ICAB (E. ROSSI, I) • Coordinated development of linear scaling methods for ab initio calculations with particular emphasis on chemical data transfer and handling • 6 Laboratories (Elda Rossi – CINECA –Italy, Renzo Cimiraglia - Università di Ferrara – Italy, Daniel Maynau – IRSAMC – France, José Sanchez-Marin - Universitat de Valencia – Spain, Peter Szalay - Eötvös Loránd University – Hungary, Rosa Caballol - Universitat Rovira i Virgili Spain)

  18. COMOVIT (H. LUETHI, CH) • Design and development of multimedia distributed software to handle 3D molecular information of ab initio origin • 6 Laboratories (Hans Peter Luethi, ETH - Zurich - CH)

  19. SURFACE Construction of the Potential Energy Surface PROPERTIES DYNAMICS Dynamical properties Calculation Calculation of Averaged quantities Good Results? no yes end The architecture of the Simulator

  20. Electronic Structure calculation and representation • Isolated (gas phase) small molecules • Isolated (gas phase) large molecules • Condensed phase and solid state calculations • Topological studies • Modeling and functional representations of the potential energy surfaces

  21. Molecular Dynamics calculations • Exact quantum dynamics for small systems • Semiclassical and mixed classical-quantum for intermediate systems • QM/MM and Car Parrinello • Classical dynamics

  22. Observable Properties • Structure and stability calculations for aggregates of various sizes • Kinetics and fluid dynamics calculations • Thermodynamics properties • Direct Monte Carlo calculations • Condensed phase and liquid crystals • Cross sections and rate coefficients

  23. Electronic Structure Programs • Small molecules (GAMESS-UK, GAMESS US, MOLPRO) • Large molecules (GAUSSIAN03) • Topological analysis of the interactions (AIMPAC, TOPOND) • Modelling and fitting of the potential energy surfaces (FITTING)

  24. Molecular Dynamics Programs • Car-Parrinello (CPMD) • Classical dynamics (ABCtraj, VENUS96; DL_POLY) • Quantum dynamics (TD) • Semiclassical dynamics (ABCsem)

  25. Observable Properties Programs • Direct Monte Carlo (DSMC) • Energy and angular distributions

  26. Critical Features of the Individual Programs • AB INITIO METHODS (molpro, gamess, adc, gaussian, ) resource requests are proportional to N3(N is the number of electrons) and to MD (M is the number of grid points per dimension D) for CPU and disc demand. • EMPIRICAL FORCE FIELDS (Venus, dl_poly, …) resource requests are proportional to P! (P is the number of atoms)

  27. Critical Features of the Individual Programs (ii) • DYNAMICS (APH3D, TIMEDEP, …) these programs use as input the output of the previous module most critical dependence is on the total angular momentumJ value that can increase up to several hundred units and the size of the matrices depend on 2J+1 • KINETICS PROGRAMS use dynamics results for integrating relevant time dependent applications

  28. SimulatorPrograms If VMs involved Java Applets SimGate Grid infrastructure Grid middleware The model architecture of a Simulator Ab-initio techniques, PES fitting, Molecular Dynamics Net Sockets Net Sockets Client side Polling HTTP Server side

  29. Local Platforms • Several workstations (IBM, Sun, SG, HP, ..) • Clusters of PC • Parallel machines (IBM SP, Origin, Sun multiprocessor, …) • Supercomputer centers (CINECA, EPCC, CESCA, ..)

  30. Metalaboratories components • Molecular expertise centers • Specialized software fabric (programs, interfaces, ..) • Grid middleware • Grid infrastructure • Users

  31. Virtual Monitors of theAngular Distribution of H + ICl ABCtraj: QCT for 3 body systems

  32. OH-HCl trajectory Venus: QCT for many body systems

  33. Virtual Monitor of Ar+C6H6 DL-POLY: QCT for complex systems

  34. Conclusions • A proposal to deploy a Chemistry Grid Application aimed at building molecular simulators is presented • It is based on the activities of some already established Metalaboratories in D23 COST Action, some of them already involved in EGEE activities. • It will impact all research activities in which complex simulations need to be carried out to govern advanced experiments and a priori rationalizations of real systems.

  35. START Are Ab initio computations feasible? Application taking empirical data from Databases to generate a PES NO NO SURFACE YES YES Application using Ab Initio programs for electronic structure Application using Fitting programs to generate a PES DYNAMICS SURFACE Construction of the interaction Are Ab initio computations available?

  36. integration of scattering equations SURFACE Are Quantum Dynamics Calculations unfeasible? Application using Time-Independent Quantum Techniques NO NO Single Initial State? DYNAMICS YES YES Application using Time-Dependent Quantum Techniques Application using Classical Dynamics (trajectory) Techniques PROPERTIES DYNAMICS

  37. Return to START DYNAMICS NO NO Rate Coefficients Virtual Monitor YES YES Vibrational, Rotational, Angular Distribution Virtual Monitors Cross Section Virtual Monitor Do measured and calculated properties agree ? NO YES Save the data of Virtual Monitors STOP PROPERTIES Reconstruction of reaction properties State to State observable quantities? State Specific observable quantities? PROPERTIES

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