Computational Chemistry Robots ACS Sep 2005 Computational Chemistry Robots ACS Sep 2005...
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Computational Chemistry Robots
ACS Sep 2005
Computational Chemistry Robots
ACS Sep 2005
Computational ChemistryRobots
J. A. Townsend, P. Murray-Rust,
S. M. Tyrrell, Y. Zhang
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Computational Chemistry Robots
ACS Sep 2005
•Can high-throughput computation provide a reliable “experimental” resource for
molecular properties?
•Can protocols be automated?
•Can we believe the results?
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Computational Chemistry Robots
ACS Sep 2005
Aspects of complete automation
• Humans must validate protocols rather than individual data
• Low rates of error must be addressed• Users should know the rates of error and degree
of conformance
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Computational Chemistry Robots
ACS Sep 2005
Approaches to conformance
• Explore limits of job behaviour (times, convergence, etc.)
• Analyse reproducibility• Vary and analyse effects of parameters and
algorithms• Compare output with other “measurements” of
same quantity
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Computational Chemistry Robots
ACS Sep 2005
The overall view
molecules computation dissemination
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Computational Chemistry Robots
ACS Sep 2005
The overall view
molecules computation dissemination
Check results
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Computational Chemistry Robots
ACS Sep 2005
Components of System
• Workflow for management of jobs (Taverna)• Natural Language Processing based parsing of
outputs (JUMBOMarker)• Pairwise comparison of data sets (R)• Analysis of mean and variance• Detection and analysis of outliers
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Computational Chemistry Robots
ACS Sep 2005
Computing the NCI database
MOPACPM5a
aMOPAC PM5 – collaboration with J.J.P. Stewart
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Computational Chemistry Robots
ACS Sep 2005
Protocol
Log Files
Parse
SystemCrashes
ScienceErrors
Analysis
PathologicalBehaviour
Statistics
Other Science DisseminateResults
UnsuitableData
ProgramCrashes
InformDeveloper
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Computational Chemistry Robots
ACS Sep 2005
Taverna
•Workflow programs allow a series of small tasks to be linked together to develop more complex tasks
•Open Source
•myGRID, eScience
•European Bioinformatics Institute
•University of Manchester
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Computational Chemistry Robots
ACS Sep 2005
An Example Taverna Workflow
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Computational Chemistry Robots
ACS Sep 2005
Parsing Log Files to CMLCoordinates
Molecular
Formula
Calculation Type
Point Group
Dipole
Total Energy
Computational Chemistry Log Files
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Computational Chemistry Robots
ACS Sep 2005
CompChemOutput
Coordinates
Energy Levels
Vibrations
Coordinates
Energy Level
Vibration
CML File
CMLCore
CMLCore
CMLComp
CMLSpect
Input/jobControl General
Parsers
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Computational Chemistry Robots
ACS Sep 2005
Dissemination of results
LOG FILE CML FILE HUMAN DISPLAY
WWMM* Server and DSpace Outside world
JUMBOMarker
NLP-based log file parser
* World Wide Molecular Matrix
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Computational Chemistry Robots
ACS Sep 2005
InChI: IUPAC International Chemical Identifier
A non-proprietary unique identifier for the representation of chemical structures.
A normal, canonicalised and serialised form of a chemical connection table.
InChI FAQ: http://wwmm.ch.cam.ac.uk/inchifaq/
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Computational Chemistry Robots
ACS Sep 2005
Proteus molecules*
Calculation
JUNK Cured by MOPAC
* Proteus was a shape changing ocean deity
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Computational Chemistry Robots
ACS Sep 2005
Proteus molecules
Calculation
Input JUNK
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Computational Chemistry Robots
ACS Sep 2005
How do we know our results are valid?
ComputationalMethod 1
ComputationalMethod 2
Experiment
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Computational Chemistry Robots
ACS Sep 2005
J.J.P. Stewart’s example
Calculated Hf – Expt Hf
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Computational Chemistry Robots
ACS Sep 2005
GAMESS
MOPACresults
GAMESSa
631G*B3LYP
Log Files
a Project with Kim Baldridge and Wibke Sudholt
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Computational Chemistry Robots
ACS Sep 2005
Protocol
Log Files
Parse
SystemCrashes
ScienceErrors
Analysis
PathologicalBehaviour
Statistics
Other Science DisseminateResults
UnsuitableData
ProgramCrashes
InformDeveloper
![Page 22: Computational Chemistry Robots ACS Sep 2005 Computational Chemistry Robots ACS Sep 2005 Computational Chemistry Robots J. A. Townsend, P. Murray-Rust,](https://reader035.fdocuments.net/reader035/viewer/2022062314/56649d805503460f94a65056/html5/thumbnails/22.jpg)
Computational Chemistry Robots
ACS Sep 2005
Repeat runs, different methods
Multiple runs give same final structure from same input
Changing memory allocation doesn’t make a difference
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Computational Chemistry Robots
ACS Sep 2005
Pathological behaviour - Early detection
100 min 631G*, B3LYP 200 min
15 min 631G*, B3LYP 10080 min
divinyl ether trans-Crotonaldehyde
Z matrix
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Computational Chemistry Robots
ACS Sep 2005
Times to run jobs
0
40,000
80,000
120,000
0.E+00 5.E+08 1.E+09
(n basis functions)4
time
/ s
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Computational Chemistry Robots
ACS Sep 2005
Analysis of different computational methods
Mean - Overall difference
Normality - Distribution of values
Outliers - Unusual molecules?
Variance - Spread of the data, depends
on both distributions.
(standard deviation)
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Computational Chemistry Robots
ACS Sep 2005
Probability Plot (Normal QQ plot)
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Computational Chemistry Robots
ACS Sep 2005
Mean of distribution(Approx - 0.03 Å)
Range over whichsample distribution is approximately normal
Outliers
Probability Plot (Normal QQ plot)S.D. 0.020 Å
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Computational Chemistry Robots
ACS Sep 2005
All bonds* r (MOPAC – GAMESS) / Å
* Excludes bonds to Hydrogenc
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Computational Chemistry Robots
ACS Sep 2005
All bonds* r (MOPAC – GAMESS) / Å
Good agreement
Nearly normal
Outliers
S.D. 0.005 Å
* Excludes bonds to Hydrogenc
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Computational Chemistry Robots
ACS Sep 2005
NN
O
2-
Bad molecules and data usually cause outliers
Na
P
O
OH
H
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Computational Chemistry Robots
ACS Sep 2005
Mean r (M - G) / Å Standard Error of the Mean / Å
C N O F S Cl
C-0.006 0.020 -0.010 -0.014 -0.040 -0.037
0.000 0.000 0.000 0.001 0.001 0.001
N 0.006 -0.037 -0.055
0.001 0.001 0.009
O -0.087 -0.070
0.004 0.014
All values given to 3 significant figures
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Computational Chemistry Robots
ACS Sep 2005
r CC bonds (M - G) / Å
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Computational Chemistry Robots
ACS Sep 2005
r CC bonds (M - G) / Å
Good agreement
Nearly normal Outliers
S.D. 0.013 Å
JUNK
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Computational Chemistry Robots
ACS Sep 2005
Selection of molecules with C C r (M - G) > 0.05 Angstroms
CF3
OH
OH CF3
H CF3
OCF3N
H
NH2
OHOHFF
OH CHF2
O
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Computational Chemistry Robots
ACS Sep 2005
Y = 0.0277 X – 0.0061
Non aromatic C C bonds adjacent to CFn
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Computational Chemistry Robots
ACS Sep 2005
r NN bonds (M - G) / Å
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Computational Chemistry Robots
ACS Sep 2005
Good agreement
Nearly normal
Kink
S.D. 0.022 Å
r NN bonds (M - G) / Å
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Computational Chemistry Robots
ACS Sep 2005
Density plot of r NN bonds (M - G) / Å
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Computational Chemistry Robots
ACS Sep 2005
LEFT
RIGHT
Density plot of r NN bonds (M - G) / Å
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Computational Chemistry Robots
ACS Sep 2005
Most common fragments found in Left set but not Right set
N
NC(sp3)C(sp3)
(sp3)S(sp2)
N(ar)
N (ar)
C(sp2)
S(sp2)
N(ar)
N (ar)
C(sp2)
Or
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Computational Chemistry Robots
ACS Sep 2005
GAMESS
Log Files
Comparison of theory and experiment
CIF*
CIF*
CIF*
CIF*
CIF*
CIF 2 CML
* CIF: Crystallographic Information File
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Computational Chemistry Robots
ACS Sep 2005
Reading Acta Crystallographica Section E
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Computational Chemistry Robots
ACS Sep 2005
All bonds* r (Cryst. – GAMESS) /Å Single molecules, no disorder
* Excludes bonds to Hydrogenc
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Computational Chemistry Robots
ACS Sep 2005
All bonds* r (Cryst. – GAMESS) /Å Single molecules, no disorder
Mean r - 0.011 Å
Nearly normalOutliers
S.D. 0.014 Å
* Excludes bonds to Hydrogenc
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Computational Chemistry Robots
ACS Sep 2005
r CC bonds (C – G) /Å
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Computational Chemistry Robots
ACS Sep 2005Mean r- 0.01 Å
Nearly normal
S.D. 0.009 Å
r CC bonds (C – G) /Å
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Computational Chemistry Robots
ACS Sep 2005
r CO bonds (C – G) /Å
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Computational Chemistry Robots
ACS Sep 2005
Good agreement
Nearly normalOutliers ?
S.D. 0.011 Å
r CO bonds (C – G) /Å
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Computational Chemistry Robots
ACS Sep 2005
r = +0.08 Å
Chemistry can cause outliers
H movement
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Computational Chemistry Robots
ACS Sep 2005
Conclusions
• Protocols can be automated
• Machines can highlight unusual behaviour,
geometries and distribution of results for
humans to consider
•Computational programs can provide high
quality “experimental” molecular properties
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Computational Chemistry Robots
ACS Sep 2005
Thanks
J.J.P. Stewart
Kim Baldridge
Wibke Sudholt
Simon Tyrrell
Yong Zhang
Peter Murray-Rust
Unilever
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Computational Chemistry Robots
ACS Sep 2005
Questions
Homepage: http://wwmm.ch.cam.ac.uk
InChI FAQ: http://wwmm.ch.cam.ac.uk/inchifaq
R: http:// www.r-project.org
Taverna: http://taverna.sourceforge.net/
MOPAC 2002: http://www.cachesoftware.com/mopac/
GAMESS: http:// www.msg.ameslab.gov/GAMESS/GAMESS.html