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Development of Integrated Environment for Computational Chemistry and Molecular Modeling Dr. Vladislav Vassiliev Supercomputer Facility, The Australian.

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Presentation on theme: "Development of Integrated Environment for Computational Chemistry and Molecular Modeling Dr. Vladislav Vassiliev Supercomputer Facility, The Australian."— Presentation transcript:

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 June, A part of the APAC grid July, … - 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 JMolEditor Shelves Gaussian Amber Gamess Gromacs Job submission Job Monitoring Getting results Providers: GT2 GT4 SSH Local Tripos Mol2 PDB Input File Formats Input File Preparation Gaussian Amber Gamess Gromacs Database JMolEditor There are two standalone programs, JMolEditor and Shelves Analysis

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

9 The most popular Computational Chemistry Programs on the National Facility (1920 CPUs) Chemistry SoftwareUsage (%) gaussian18.1 gamess0.01 mopac0.32 amber3.1 gromacs1.02 charmm3.8 molpro2.1 vasp8.5 namd4.4 nwchem0.03 siesta1.9 Our primary targets are the most popular programs in the Computational Chemistry community Of total wall time on the Altix cluster (1920 CPUs)

10 Shelves (Dr. Andrey Bliznyuk) On the web:

11 JMolEditor – Java Molecular Editor On the web: More than 1000 downloads since mid- April from 50 countries

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

13 JMolEditor & GridChem https://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 PBD Gromacs MDL Molfile Tripos Mol2 XMol XYZ etc. PDB Format: ATOM 1 N ALA ATOM 2 CA ALA ATOM 3 C ALA ATOM 4 O ALA ATOM 5 CB ALA MDL Molfile C H C H X, Y, Z coordinates

17 “Complex” Computational Chemistry Formats: ADF Define ZERO = 0.0 R1 = R2 = R3 = ALPHA = 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 “Complex” Computational Chemistry Formats: Q-Chem $molecule 0 1 c1 c2 c1 cc c3 c2 cc c c4 c3 cc c c1 0.0 c5 c4 cc c c2 0.0 c6 c5 cc c c3 0.0 h1 c1 hc c c h2 c2 hc c c h3 c3 hc c c h4 c4 hc c c h5 c5 hc c c h6 c6 hc c c cc = hc = $end

19 “Complex” Computational Chemistry Formats: GAMESS $DATA Tetramethyleneethane...UHF/DZP DN 2 CARBON CARBON HYDROGEN HYDROGEN $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 Simple Gaussian Input Editor Gaussian Gamess Mopac Amber Gromacs

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 Common options for all programs Program specific options Provider Specific Options Scheduler Specific Options All complexities of the Grid job submission are hidden behind a dialog

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 1.charge.off 2.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”: H igh 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 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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