describes how to design and implement a protocol for high-through put computation

1. Computational Chemistry Robots ACS Sep 2005 Computational Chemistry Robots J. A. Townsend, P. Murray-Rust, S. M. Tyrrell, Y. Zhang [email_address]

5. The overall view molecules computation dissemination

6. The overall view molecules computation dissemination Check results

8. Computing the NCI database MOPAC PM5 a a MOPAC PM5 – collaboration with J.J.P. Stewart

9. Protocol Log Files Parse System Crashes Science Errors Analysis Pathological Behaviour Statistics Other Science Disseminate Results Unsuitable Data Program Crashes Inform Developer

11. An Example Taverna Workflow

12. Parsing Log Files to CML Coordinates Molecular Formula Calculation Type Point Group Dipole Total Energy Computational Chemistry Log Files

13. CompChem Output Coordinates Energy Levels Vibrations Coordinates Energy Level Vibration CML File CMLCore CMLCore CMLComp CMLSpect Input/jobControl General Parsers

14. 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

16. Proteus molecules * Calculation JUNK Cured by MOPAC * Proteus was a shape changing ocean deity

17. Proteus molecules Calculation Input JUNK

18. How do we know our results are valid? Computational Method 1 Computational Method 2 Experiment

19. J.J.P. Stewart’s example Calculated  H f – Expt  H f

20. GAMESS MOPAC results GAMESS a 631G* B3LYP Log Files a Project with Kim Baldridge and Wibke Sudholt

21. Protocol Log Files Parse System Crashes Science Errors Analysis Pathological Behaviour Statistics Other Science Disseminate Results Unsuitable Data Program Crashes Inform Developer

22. Repeat runs, different methods Multiple runs give same final structure from same input Changing memory allocation doesn’t make a difference

23. Pathological behaviour - Early detection 100 min 631G*, B3LYP 200 min 15 min 631G*, B3LYP 10080 min divinyl ether trans-Crotonaldehyde Z matrix

24. Times to run jobs

25. 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)

26. Probability Plot (Normal QQ plot)

27. Mean of distribution (Approx - 0.03 Å ) Range over which sample distribution is approximately normal Outliers Probability Plot (Normal QQ plot) S.D. 0.020 Å

28. All bonds*  r (MOPAC – GAMESS) / Å * Excludes bonds to Hydrogenc

29. All bonds*  r (MOPAC – GAMESS) / Å Good agreement Nearly normal Outliers S.D. 0.005 Å * Excludes bonds to Hydrogenc

30. 2- Bad molecules and data usually cause outliers Na P O O H H

31. Mean  r (M - G) / Å Standard Error of the Mean / Å All values given to 3 significant figures 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

32.  r CC bonds (M - G) / Å

33.  r CC bonds (M - G) / Å Good agreement Nearly normal Outliers S.D. 0.013 Å JUNK

34. Selection of molecules with C C  r (M - G) > 0.05 Angstroms

35. Y = 0.0277 X – 0.0061 Non aromatic C C bonds adjacent to CF n

36.  r NN bonds (M - G) / Å

37. Good agreement Nearly normal Kink S.D. 0.022 Å  r NN bonds (M - G) / Å

38. Density plot of  r NN bonds (M - G) / Å

39. LEFT RIGHT Density plot of  r NN bonds (M - G) / Å

40. Most common fragments found in Left set but not Right set C(sp 3 ) C(sp 3 ) (sp 3 ) S(sp 2 ) N(ar) N (ar) C(sp 2 ) S(sp 2 ) N(ar) N (ar) C(sp 2 ) Or

41. GAMESS Log Files Comparison of theory and experiment CIF* CIF* CIF* CIF* CIF* CIF 2 CML * CIF: Crystallographic Information File

42. Reading Acta Crystallographica Section E

43. All bonds*  r (Cryst. – GAMESS) / Å Single molecules, no disorder * Excludes bonds to Hydrogenc

44. All bonds*  r (Cryst. – GAMESS) / Å Single molecules, no disorder Mean  r - 0.011 Å Nearly normal Outliers S.D. 0.014 Å * Excludes bonds to Hydrogenc

45.  r CC bonds (C – G) / Å

46. Mean  r - 0.01 Å Nearly normal S.D. 0.009 Å  r CC bonds (C – G) / Å

47.  r CO bonds (C – G) / Å

48. Good agreement Nearly normal Outliers ? S.D. 0.011 Å  r CO bonds (C – G) / Å

49.  r = +0.08 Å Chemistry can cause outliers H movement

51. Thanks J.J.P. Stewart Kim Baldridge Wibke Sudholt Simon Tyrrell Yong Zhang Peter Murray-Rust Unilever

52. 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