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Development of Integrated Environment for Computational Chemistry and Molecular Modeling

Development of Integrated Environment for Computational Chemistry and Molecular Modeling. Dr. Vladislav Vassiliev Supercomputer Facility, The Australian National University, ACT 0200, Canberra, Australia. Purposes. Computational resources. Client.

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Development of Integrated Environment for Computational Chemistry and Molecular Modeling

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  1. Development of Integrated Environment for Computational Chemistry and Molecular Modeling Dr. Vladislav Vassiliev Supercomputer Facility, The Australian National University, ACT 0200, Canberra, Australia

  2. Purposes Computational resources Client • Simplified access to computational resources (data transfer, job submission/monitoring) • Visualization of chemistry file formats and calculated results • Preparation of input files for popular programs • Analysis of calculated results

  3. A bit of History • 2004- June, 2007 - A part of the APAC grid • July, 2007 - … - A part of the ICI ICI – Interoperation and Collaboration Infrastructure

  4. People Involved • Dr Andrey Bliznyuk, ANUSF • Dr Vladislav Vassiliev, ANUSF • Dr Zhongwu Zhou, Swinburne Uni (until July) • GridChem (in US): There are about 15 people (including students and staff from 5 sites) involved about 20-40% each. Most students are 50% i.e. they work 20 hrs a week during school year.

  5. What does it mean “Integrated Environment”? • An integrated environment for Molecular Modelling should assist a full production cycle in Computational Chemistry • input data preparation and visualization • job submission to the grid • job status monitoring • retrieving, analysis and visualization of the final results • and preparation of high quality graphics for publications.

  6. Our Collaborators • Prof. Leo Radom, University of Sydney • Prof. Jill Gready, ANU • Dr. Michelle Coote, ANU • Dr. Rob Stranger, ANU • Dr. Mark Buntine, The University of Adelaide

  7. “Integrated Environment”: Overall Architecture There are two standalone programs, JMolEditor and Shelves Providers: GT2 GT4 SSH Local Database PDB JMolEditor Tripos Mol2 Gaussian Job submission Job Monitoring Getting results Gaussian Amber Input File Formats Input File Preparation Amber Gamess Shelves Gromacs Gamess Analysis JMolEditor Gromacs

  8. “Integrated Environment”: Implementing a Full Production Cycle Structure Preparation Input File Preparation Job Submission Output Files Download Analysis of the Calculated Results Job Status Monitoring

  9. The most popular Computational Chemistry Programs on the National Facility (1920 CPUs) Of total wall time on the Altix cluster (1920 CPUs) Our primary targets are the most popular programs in the Computational Chemistry community

  10. Shelves (Dr. Andrey Bliznyuk) On the web: http://sf.anu.edu.au/~aab900/grid

  11. JMolEditor – Java Molecular Editor More than 1000 downloads since mid-April from 50 countries On the web: http://sf.anu.edu.au/~vvv900/cct/appl/jmoleditor/index.html

  12. JMolEditor on the Web Mopac2007 Home Page Gordon group/GAMESS & PC GAMESS Home Pages World Index of BioMolecular Visualization Resources

  13. JMolEditor & GridChemhttps://www.gridchem.org/ The "Computational Chemistry Grid" (CCG) is a virtual organization that provides access to high performance computing resources for computational chemistry with distributed support and services, intuitive interfaces and measurable quality of service. The CCG client, GridChem, is a Java desktop application that provides an interface to integrate the hardware, software and middleware resources necessary to solve quantum chemistry problems using grid technologies.

  14. “Integrated Environment”: Rich User Interface High-performance 3D rendering Intuitive interface for unexperienced users

  15. “Integrated Environment”: Support for popular Computational Chemistry Formats Gaussian GAMESS Mopac PBD Tripos Mol2 Amber Gromacs etc.

  16. “Simple” Computational Chemistry Formats MDL Molfile 22 26 0 0 0 0 0 0 0 0 0 -1.1240 -0.9460 -0.0810 C 0 0 0 0 0 0 0 0 0 1 -1.6382 -1.7296 -0.4297 H 0 0 0 0 0 0 0 0 0 0 -1.1850 1.2860 0.0050 C 0 0 0 0 0 0 0 0 0 3 -1.7626 2.0974 -0.0840 H 0 0 0 0 0 0 0 0 0 0 X, Y, Z coordinates PBD Gromacs MDL Molfile Tripos Mol2 XMol XYZ etc. X, Y, Z coordinates PDB Format: ATOM 1 N ALA 1 6.905 -5.627 16.260 ATOM 2 CA ALA 1 6.234 -4.818 15.182 ATOM 3 C ALA 1 6.995 -3.490 15.087 ATOM 4 O ALA 1 7.597 -3.018 16.076 ATOM 5 CB ALA 1 4.719 -4.843 15.275

  17. “Complex” Computational Chemistry Formats: ADF Define ZERO = 0.0 R1 = 2.406 R2 = 2.074 R3 = 1.100 ALPHA = 108.215 X1 = ZERO Y1 = ZERO Z1 = ZERO X2 = ZERO Y2 = ZERO Z2 = -R1 X3 = ZERO Y3 = ZERO Z3 = R2 X4 = sqrt(6)*(R3/3)*sqrt(1-cos(ALPHA)) Y4 = ZERO Z4 = R2+sqrt(3)*(R3/3)*sqrt(1+(2*cos(ALPHA))) X5 = -sqrt(6)*(R3/6)*sqrt(1-cos(ALPHA)) Y5 = sqrt(2)*(R3/2)*sqrt(1-cos(ALPHA)) Z5 = R2+sqrt(3)*(R3/3)*sqrt(1+(2*cos(ALPHA))) X6 = -sqrt(6)*(R3/6)*sqrt(1-cos(ALPHA)) Y6 = -sqrt(2)*(R3/2)*sqrt(1-cos(ALPHA)) Z6 = R2+sqrt(3)*(R3/3)*sqrt(1+(2*cos(ALPHA))) End Atoms Hg X1 Y1 Z1 Br X2 Y2 Z2 C X3 Y3 Z3 H X4 Y4 Z4 H X5 Y5 Z5 H X6 Y6 Z6 End

  18. $molecule 0 1 c1 c2 c1 cc c3 c2 cc c1 120.0 c4 c3 cc c2 120.0 c1 0.0 c5 c4 cc c3 120.0 c2 0.0 c6 c5 cc c4 120.0 c3 0.0 h1 c1 hc c2 120.0 c3 180.0 h2 c2 hc c3 120.0 c4 180.0 h3 c3 hc c4 120.0 c5 180.0 h4 c4 hc c5 120.0 c6 180.0 h5 c5 hc c6 120.0 c1 180.0 h6 c6 hc c1 120.0 c2 180.0 cc = 1.3862 hc = 1.0756 $end “Complex” Computational Chemistry Formats: Q-Chem

  19. “Complex” Computational Chemistry Formats: GAMESS $DATA Tetramethyleneethane...UHF/DZP DN 2 CARBON 6.0 0.755500 CARBON 6.0 1.421360 1.128718 0.466377 HYDROGEN 1.0 2.494295 1.176481 0.468728 HYDROGEN 1.0 0.882613 1.996977 0.790509 $END

  20. “Integrated Environment”: On-line and in-built help system and tutorials Tracking Help Help

  21. “Integrated Environment”: Molecular Builder/Editor Adding/deleting Atoms Adding Fragments Adding Molecules Modifying atoms, bonds, angles, dihedral angles Automatic filling of empty valences with hydrogens

  22. “Integrated Environment”:Preparation of input files for popular programs • Gaussian • Gamess • Mopac • Amber • Gromacs Simple Gaussian Input Editor

  23. “Integrated Environment”:Preparation of input files for popular programs • Gaussian (Shelves) Advanced Gaussian Input Editor

  24. “Integrated Environment”: Preparation of input files for popular programs • Gamess (Shelves)

  25. “Integrated Environment”: Preparation of input files for popular programs • Mopac (Shelves)

  26. “Integrated Environment”: Preparation of input files for popular programs • Molpro (Shelves)

  27. “Integrated Environment”: Job Submission All complexities of the Grid job submission are hidden behind a dialog Common options for all programs Provider Specific Options Scheduler Specific Options Program specific options

  28. “Integrated Environment”: Job Status Monitoring To download output files To kill selected jobs

  29. “Integrated Environment”: Visualizing Volumetric Data (Gaussian cubes)

  30. Object Oriented Graphics Library(OOGL) File Format

  31. Object Oriented Graphics Library(OOGL) File Format and Gaussian #p hf/6-31g(d) SCRF(PCM,Solvent=Water,Read) test Toluene, Onsager Model 0 1 C C 1 B1 ... ITERATIVE RADII=Pauling PCMDOC GEOMVIEW • charge.off • tesserae.off

  32. Object Oriented Graphics Library(OOGL) File Format and Gaussian tesserae.off

  33. Object Oriented Graphics Library(OOGL) File Format and Gaussian charge.off

  34. Object Oriented Graphics Library(OOGL) File Format and Gaussian

  35. “Integrated Environment”: High quality graphics for publishing: Image Capture

  36. “Integrated Environment”: High quality graphics for publishing: POV-Ray Generated by POV-Ray (The Persistence of Vision Raytracer)

  37. New Feature Easy access to files on remote computers

  38. System requirements • Mac OS All is already there… • MS Windows and Linux 1) The Java Runtime Environment (JRE)≥ 1.5 2) Download and install Java3d (freeware optional component)

  39. Download Site for JMolEditor • http://sf.anu.edu.au/~vvv900/cct/appl/jmoleditor/index.html Option 1: Download a program to run it on a desktop (Java jar file) Option 2: Run from a website using Java Web Start • On-line Help

  40. What will be next? • Support for more Computational Chemistry Programs (visualization, input files preparation, analysis of final results) • Gaussian/ONIOM support • Animation & analysis of the Molecular Dynamics trajectrories (cluster analysis) • Easy access to files on remote computers • Z-Matrix Editor • Post-processing of Gaussian IRC output files (plotting the energies along the scan, extracting geometries) • Adding new features according to the user’s requests…

  41. What can we do for you? • Do you need support for any specific chemical file format to visualize it? • Do you need the ability to save your data into any specific chemical file format? • Analysis of the calculated results?

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