Development of Integrated Environment for Computational Chemistry and Molecular Modeling

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

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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

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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.

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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.

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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

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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
Gamess
Gromacs
Analysis
Gromacs
JMolEditor
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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
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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
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Shelves (Dr. Andrey Bliznyuk)
On the web http//sf.anu.edu.au/aab900/grid
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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
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JMolEditor on the Web
Mopac2007 Home Page
Gordon group/GAMESS PC GAMESS Home Pages
World Index of BioMolecular Visualization
Resources
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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.
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Integrated Environment Rich User Interface
High-performance 3D rendering
Intuitive interface for unexperienced users
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Integrated Environment Support for popular
Computational Chemistry Formats
Gaussian GAMESS Mopac PBD Tripos
Mol2 Amber Gromacs etc.
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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
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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
R2sqrt(3)(R3/3)sqrt(1(2cos(ALPHA))) X5
-sqrt(6)(R3/6)sqrt(1-cos(ALPHA)) Y5
sqrt(2)(R3/2)sqrt(1-cos(ALPHA)) Z5
R2sqrt(3)(R3/3)sqrt(1(2cos(ALPHA))) X6
-sqrt(6)(R3/6)sqrt(1-cos(ALPHA)) Y6
-sqrt(2)(R3/2)sqrt(1-cos(ALPHA)) Z6
R2sqrt(3)(R3/3)sqrt(1(2cos(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
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Complex Computational Chemistry Formats Q-Chem
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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
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Integrated Environment On-line and in-built
help system and tutorials
Tracking Help
Help
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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
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Integrated Environment Preparation of input
files for popular programs

• Gaussian
• Gamess
• Mopac
• Amber
• Gromacs

Simple Gaussian Input Editor
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Integrated Environment Preparation of input
files for popular programs

• Gaussian (Shelves)

Advanced Gaussian Input Editor
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Integrated Environment Preparation of input
files for popular programs

• Gamess (Shelves)

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Integrated Environment Preparation of input
files for popular programs

• Mopac (Shelves)

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Integrated Environment Preparation of input
files for popular programs

• Molpro (Shelves)

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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
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Integrated Environment Job Status Monitoring
To download output files
To kill selected jobs
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Integrated Environment Visualizing Volumetric
Data (Gaussian cubes)
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Object Oriented Graphics Library (OOGL) File
Format
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Object Oriented Graphics Library (OOGL) File
Format and Gaussian
p hf/6-31g(d) SCRF(PCM,SolventWater,Read)
test Toluene, Onsager Model 0 1 C C 1
B1 ... ITERATIVE RADIIPauling PCMDOC GEOMVIEW

• charge.off
• tesserae.off

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Object Oriented Graphics Library (OOGL) File
Format and Gaussian
tesserae.off
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Object Oriented Graphics Library (OOGL) File
Format and Gaussian
charge.off
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Object Oriented Graphics Library (OOGL) File
Format and Gaussian
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Integrated Environment High quality graphics
for publishing Image Capture
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Integrated Environment High quality graphics
for publishing POV-Ray
Generated by POV-Ray (The Persistence of Vision
Raytracer)
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New Feature Easy access to files on remote
computers
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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)

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Download Site for JMolEditor

• http//sf.anu.edu.au/vvv900/cct/appl/jmoleditor/i
  ndex.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

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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 users
  requests

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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?