development of integrated environment for computational chemistry and molecular modeling
DESCRIPTION
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. - PowerPoint PPT PresentationTRANSCRIPT
Development of Integrated Environment for Computational
Chemistry and Molecular Modeling
Dr. Vladislav VassilievDr. Vladislav Vassiliev
Supercomputer Facility, The Australian National University, Supercomputer Facility, The Australian National University,
ACT 0200, Canberra, AustraliaACT 0200, Canberra, Australia
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
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
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.
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.
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
“Integrated Environment”: Overall Architecture
JMolEditor
Shelves
Gaussian
Amber
Gamess
Gromacs
Job submissionJob MonitoringGetting results
Providers:GT2GT4SSHLocal
Tripos Mol2
PDB
Inpu
t Fil
e F
orm
ats
Inpu
t Fil
e P
repa
rati
on Gaussian
Amber
Gamess
Gromacs
Database
JMolEditor
There are two standalone programs,
JMolEditor and Shelves
Analysis
“Integrated Environment”: Implementing a Full Production Cycle
Structure Preparation
Input FilePreparation
Job Submission
Job Status Monitoring
Output FilesDownload
Analysis of the Calculated Results
The most popular Computational Chemistry Programs on the National Facility (1920 CPUs)
Chemistry Software Usage (%)gaussian 18.1gamess 0.01mopac 0.32amber 3.1
gromacs 1.02charmm 3.8molpro 2.1
vasp 8.5namd 4.4
nwchem 0.03siesta 1.9
Our primary targets are the most popular
programs in the Computational
Chemistry community
Of total wall time on the Altix
cluster (1920 CPUs)
Shelves (Dr. Andrey Bliznyuk)
On the web: http://sf.anu.edu.au/~aab900/grid
JMolEditor – Java Molecular Editor
On the web: http://sf.anu.edu.au/~vvv900/cct/appl/jmoleditor/index.html
More than 1000 downloads since mid-April from 50 countries
JMolEditor on the Web
World Index of BioMolecular Visualization Resources
Mopac2007 Home Page
Gordon group/GAMESS & PC GAMESS Home Pages
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.
“Integrated Environment”: Rich User Interface
High-performance 3D
rendering
Intuitive Intuitive interface for interface for
unexperienced unexperienced usersusers
“Integrated Environment”: Support for popular Computational
Chemistry Formats
Gaussian
GAMESS
Mopac
PBD
Tripos Mol2
Amber
Gromacs
etc.
“Simple” Computational Chemistry Formats
PBD
Gromacs
MDL Molfile
Tripos Mol2
XMol XYZ
etc.
PDB Format:ATOM 1 N ALA 1 6.905 -5.627 16.260ATOM 2 CA ALA 1 6.234 -4.818 15.182ATOM 3 C ALA 1 6.995 -3.490 15.087ATOM 4 O ALA 1 7.597 -3.018 16.076ATOM 5 CB ALA 1 4.719 -4.843 15.275
MDL Molfile22 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
X, Y, Z coordinates
“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 Z6End
“Complex” Computational Chemistry Formats: Q-Chem$molecule0 1c1c2 c1 ccc3 c2 cc c1 120.0c4 c3 cc c2 120.0 c1 0.0c5 c4 cc c3 120.0 c2 0.0c6 c5 cc c4 120.0 c3 0.0h1 c1 hc c2 120.0 c3 180.0h2 c2 hc c3 120.0 c4 180.0h3 c3 hc c4 120.0 c5 180.0h4 c4 hc c5 120.0 c6 180.0h5 c5 hc c6 120.0 c1 180.0h6 c6 hc c1 120.0 c2 180.0 cc = 1.3862hc = 1.0756$end
“Complex” Computational Chemistry Formats: GAMESS
$DATATetramethyleneethane...UHF/DZPDN 2 CARBON 6.0 0.755500CARBON 6.0 1.421360 1.128718 0.466377HYDROGEN 1.0 2.494295 1.176481 0.468728HYDROGEN 1.0 0.882613 1.996977 0.790509$END
“Integrated Environment”: On-line and in-built help system and tutorials
Tracking Help
Help
“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
“Integrated Environment”: Preparation of input files for popular programs
Simple Gaussian Input Editor
• Gaussian
• Gamess
• Mopac
• Amber
• Gromacs
“Integrated Environment”: Preparation of input files for popular programs
• Gaussian (Shelves)
Advanced Gaussian Input Editor
“Integrated Environment”: Preparation of input files for popular programs
• Gamess (Shelves)
“Integrated Environment”: Preparation of input files for popular programs
• Mopac (Shelves)
“Integrated Environment”: Preparation of input files for popular programs
• Molpro (Shelves)
“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
“Integrated Environment”: Job Status Monitoring
To download output files To kill selected
jobs
“Integrated Environment”: Visualizing Volumetric Data (Gaussian cubes)
Object Oriented Graphics Library (OOGL) File Format
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
...
ITERATIVERADII=PaulingPCMDOCGEOMVIEW
1. charge.off
2. tesserae.off
Object Oriented Graphics Library (OOGL) File Format and Gaussian
tesserae.off
Object Oriented Graphics Library (OOGL) File Format and Gaussian
charge.off
Object Oriented Graphics Library (OOGL) File Format and Gaussian
“Integrated Environment”: High quality graphics for publishing: Image Capture
“Integrated Environment”: High quality graphics for publishing: POV-Ray
Generated by POV-Ray (The Persistence of Vision Raytracer)
New Feature Easy access to files on remote
computers
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)
Download Site for JMolEditor
• http://sf.anu.edu.au/~vvv900/cct/appl/jmoleditor/index.htmlOption 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
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…
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?