Development of Integrated Environment for Computational Chemistry and Molecular Modeling

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?