Skip to main content
SpringerLink
Log in

Molecular simulation and the collaborative computational projects

  • Published:
The European Physical Journal H Aims and scope Submit manuscript

Abstract

In the late 1970s, the embryonic UK research community in molecular simulation – physicists and physical chemists – organised itself around CCP5, one of a set of Collaborative Computational Projects in different fields. CCP5 acted to develop and use the software required by an evolving and expanding scientific agenda, to exploit quickly and efficiently the revolution in computing hardware and to educate and nurture the careers of future generations of researchers in the field. This collaboration formally began in 1980, and is still fully active now, 40 years later. Today, molecular simulation techniques, many of them pioneered by CCP5, are now used very widely, including in several other CCPs in the UK’s current family of Collaborative Computational Projects. This article tells the story of molecular simulation in the UK, with CCP5 itself at centre stage, using the written records in the CCP archives. The authors were, or are, all personally involved in this story.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  1. Allan R.J. (ed.) 1995, HPC Profile, Issue 1 (Daresbury Laboratory)

  2. Allan R.J. and Guest M.F. 1990, Introduction to the INTEL iPSC/860 and iPSC/2 Supercomputers, Version 1.0 (Daresbury Laboratory)

  3. Allan R.J. and Guest M.F. 1992a, The Intel iPSC/2, an Introductory Guide to the Hypercube, Revision A (Daresbury Laboratory)

  4. Allan R.J. and Guest M.F. 1992b, The Intel iPSC/2, an Introductory Guide to Hypercube Applications, Revision B (Daresbury Laboratory)

  5. Allen M.P. 2019, http://www.sandia.gov/ASCI/; http://www.llnl.gov/asci/ private communication

  6. Baccia B., Danelutto M., Pelagatti S. and Vanneschi M. 1999, Parallel Computing 25: 1827

    Article  Google Scholar 

  7. Battimelli G. and Ciccotti G. 2018, Eur. Phys. J. H 43: 303

    Article  Google Scholar 

  8. Boateng H.A. and Todorov I.T. 2015, J. Chem. Phys. 142: 034117

    Article  ADS  Google Scholar 

  9. Brooks B.R., Bruccoleri R.E., Olafson B.D., States D.J., Swaminathan S. and Karplus M. 1983, J. Comp. Chem. 4: 187

    Article  Google Scholar 

  10. Burke P.G. 1998, Computer Physics Communications 114: xii–xvii

    Article  Google Scholar 

  11. Burke P.G., Davies B.W. and Edwards D.P. (eds.) 1982, Some Research Applications on the Cray-1 Computer at the Daresbury Laboratory 1979-81 (Daresbury Laboratory)

  12. Bush I.J., Todorov I.T. and W. Smith 2006, Comp. Phy. Commun. 175: 323

    Article  ADS  Google Scholar 

  13. Case D.A., Cheatham T.E., Darden T., Gohlke H., Luo R., Merz K.M., Onufriev A., Simmerling C., Wang B. and Woods R. 2005, J. Comp. Chem. 26: 1668

    Article  Google Scholar 

  14. Catlow C.R.A. 1992, Research Requirements for High Performance Computing (SERC)

  15. Catlow C.R.A., Parker S.C. and Allen M.P. (eds.) 1990, Computer Modelling of Fluids Polymers and Solids (Kluwer)

  16. Catlow C.R.A. and Woodley S.M. (eds.) 2006, special issue on “High Performance Computing in Materials Chemistry”, J. Mater. Chem. 16

  17. Davies B.W. 1984, Central Computing Committee Review Working Party Report. Appendix C: a next generation Supercomputer for Academic Research. (SERC)

  18. Dove M.T., Sullivan L.A., Walker A.M., Bruin R.P., White T.O.H., Trachenko K., Murray-Rust P., Todorov I.T., Tyer R.P., Couch P.A., Kleese van Dam K. and Smith W. 2006, Mol. Sim. 32: 945

    Article  Google Scholar 

  19. Essmann U., Perera L., Berkowitz M.L., Darden T., Lee H. and Pedersen L.G. 1995, J. Chem. Phys. 103: 8577

    Article  ADS  Google Scholar 

  20. Fincham D. and Guest M.F. 1989, Computational Science Initiative; A progress Report (Daresbury Laboratory, SERC)

  21. Forty A.J. et al. (eds.) 1985, Future Facilities for Advanced Research Computing, A report of a joint working party of ABRC, UGC and the Computer Board (SERC, ISBN 0-901660-73-6)

  22. Frigo M. and Johnson S.G. 2005, Proceedings of the IEEE 93(2): 216

    Article  Google Scholar 

  23. Goodfellow J.M. 1981, Review of CCP5 Polarizability Meeting, CCP5 Information Quarterly 1:4 (Daresbury Laboratory)

  24. Guest M.F. 1986, Computational Physics and Chemistry on an FPS-164 / MAX – Experience within SERC (Daresbury, CCP/86/1)

  25. Guest M.F., Elena A.M. and Chalk A.B.G. 2019, “DL_POLY – A Performance Overview: Analysing, Understanding and Exploiting available HPC Technology”, MolecularSimulation (Taylor & Francis) special issue – “DL_POLY: Twenty-five years of molecular dynamics evolution” (in press)

  26. Hudak D.E., Ludban N., Krishnamurthy A., Gadepally V., Samsi S. and Nehrbass J. 2009, International Journal of Parallel Programming 37: 91

    Article  Google Scholar 

  27. Leslie M. 2010, Molecular Physics 106: 1567

    Article  ADS  Google Scholar 

  28. Lester W.A. 1980, Recent Developments in Computational Chemistry in the U.S.: the NRCC (National Resource for Computation in Chemistry) in: Bargon J. (ed.) Computational Methods in Chemistry, the IBM Research Symposia Series (Springer, Boston)

  29. Levesque D. and Hansen J.-P. 2019, Eur. Phys. J. H 44: 37

    Article  Google Scholar 

  30. Lindahl E., Hess B. and van der Spoel D. 2001, J. Mol. Model. 7: 306

    Article  Google Scholar 

  31. Mareschal M. 2018, Eur. Phys. J. H 43: 293

    Article  Google Scholar 

  32. Phillips J.C., Braun R., Wei Wang, Gumbart J., Tajkhorshid E., Villa E., Chipot C., Skeel R.D., Kale L., and Schulten K. 2005, J. Comput. Chem. 26: 1781

    Article  Google Scholar 

  33. Plimpton S. 1995, J. Comput. Phys. 117: 1

    Article  ADS  Google Scholar 

  34. Price S.L., Hamad S., Torrisi A., Karamertzanis P.G., Leslie M. and Catlow C.R.A. 2006, Molecular Simulation 32: 985

    Article  Google Scholar 

  35. Seaton M., Todorov I. and Afshar Y. 2013, in Parallel Computing Technologies: Lecture Notes in Computer Science, V. Malyshkin (ed.) ( Springer)

  36. Simon H. (Chair) 2005, International Review of Research Using HPC in the UK, EPSRC and DFG

  37. Smith S.J. and Sutcliffe B.T. 1997, Rev. Comput. Chem. 10: 271

    Google Scholar 

  38. Smith W. 2010, The DL_POLY Classic Molecular Simulation Package (STFC Daresbury Laboratory) https://www.ccp5.ac.uk/DL_POLY_C

  39. Smith W. and Forester T.R. 1996, J. Molecular Graphics 14: 136

    Article  Google Scholar 

  40. Smith W., Yong C.W. and Rodger P.M. 2002, Molecular Simulation 28: 385

    Article  Google Scholar 

  41. Sokhan V. 2019, private communication

  42. Taylor D.J., Hopkinson J.F.L. and Henfrey C.C.T. 1982, “The Cray-1s and the Cray Service provided by the SERC at the Daresbury Laboratory Computer”, Computer Physics Communications 26: 259

    Article  ADS  Google Scholar 

  43. Tildesley D.J. 2011, A Strategic Vision for UK e-Infrastructure (Department for Business, Innovation and Science)

  44. Tildesley D.J. 2019, private communication

  45. Todorov I.T. and Smith W. 2004, Philosophical Transactions of the Royal Society A 362: 1835

    Article  ADS  Google Scholar 

  46. Todorov I.T., Allan N.L., Purton J.A., Dove M.T. and Smith W. 2007, J. Mater. Sci. 42(6): 1920

    Article  ADS  Google Scholar 

  47. Todorov I.T., Bush I.J. and Porter A.R. 2008, Proceedings of Performance Scientific Computing (International Networking for Young Scientists, Lithuania)

  48. Todorov I.T., Ellison L.J., Seaton M.A., Smith W. 2013a, in “Multiscale Modelling Methods for Applications in Material Science” CECAM Lecture Notes, IAS Series 19

  49. Todorov I.T., Ellison L., and Smith W. 2013b, in Parallel Computing Technologies: Lecture Notes in Computer Science, V. Malyshkin (ed.) ( Springer)

  50. Todorov I.T., Smith W., Trachenko K. and Dove, M. 2006, Journal of Materials Chemistry 20: 1911, https://doi.org/10.1039/B517931A

    Article  Google Scholar 

  51. Tribello G.A., Bonomi M., Branduardi D., Camilloni C. and Bussi G. 2014, Comp. Phys. Comm. 185: 604

    Article  ADS  Google Scholar 

  52. Walker A.M., Sullivan L.A., Trachenko K., Bruin R.P., White T.O.H., Dove M.T., Tyer R.P., Todorov I.T. and Wells S.A. 2007, J. Phys.: Condens. Matter 19: 275210

    ADS  Google Scholar 

  53. Zarkadoula E., Daraszewicz S.L., Duffy D.M., Seaton M.A., Todorov I.T., Nordlund K., Dove M.T. and Trachenko K. 2014, J. Phys.: Condens. Matter 26: 085401

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. UKRI STFC Daresbury Laboratory, SCi-Tech Daresbury, Warrington, WA4 4AD, UK

    William Smith, Martyn Guest, Ilian Todorov & Paul Durham

  2. Cardiff University, Cardiff CF10 3AT, Wales, UK

    Martyn Guest

Authors
  1. William Smith
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Martyn Guest
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Ilian Todorov
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Paul Durham
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Paul Durham.

Additional information

Publisher's Note

The EPJ Publishers remain neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Smith, W., Guest, M., Todorov, I. et al. Molecular simulation and the collaborative computational projects. EPJ H 45, 259–343 (2020). https://doi.org/10.1140/epjh/e2020-10034-9

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1140/epjh/e2020-10034-9

Search

Navigation