Abstract
The two basic methods of computational chemistry, namely electronic structure calculations (quantum mechanics, QM) and those based upon force fields (molecular mechanics, MM) are now widely used, in a routine fashion, to model many aspects of the structure and reactivity of macromolecular systems. Energy minimizations based upon quite simple representations of inter—atomic interactions via MM force fields can be used to predict the geometric structure of systems having many thousands of atoms, whilst their motion, particularly important in many biological problems can be followed using molecular dynamics (MD) simulations. These latter studies are particularly computationally intensive due to the quite long time scales that often need to be simulated.
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsPreview
Unable to display preview. Download preview PDF.
References
D.A. Pearlman, D.A. Case, J.C. Caldwell, G.L. Seibel, U.C. Singh, P. Weiner, and P.A. Kollman, AMBER 4.0, University of California, San Francisco (1992).
J.D. Wright, and C.A. Reynolds, Exploiting the parallelism inherent in the windowing approach to Monte Carlo free energy perturbation calculations, J. Mol. Struct.(Theochem), in press.
W.L. Jorgensen, Boss Version 3.5, Yale University, New Haven, CT (1994).
M.J. Frisch, G.W. Trucks, H.B. Schlegel, P.M.W. Gill, B.G. Johnson, M.A. Robb, J.R. Cheeseman, T.A. Keith, G.A. Peterson, J.A. Montgomery, K. Raghavachari, M.A. Al-Laham, V.G. Zakrezewski, J.V. Ortiz, J.B. Foresman, J. Cioslowski, B.B. Stefanov, A. Nanayakkara, M. Challacombe, C.Y. Peng, P.Y. Ayala, W. Chen, M.W. Wong, J.L. Andres, E.S. Replogle, R. Gomperts, R.L. Martin, D.J. Fox, J.S. Binkley, D.J. Defrees, J. Baker, J.P. Stewart, M. Head-Gordon, C. Gonzalez, and J.A. Pople, Gaussian 94, Revision A.1, Gaussian Inc., Pittsburgh, PA (1995).
M.F. Guest, J.H. van Lenthe, J. Kendrick, K. Schoeffel, P. Sherwood, R.D. Amos, R.J. Buenker, M. Dupuis, N.C. Handy, I.H. Hillier, P.J. Knowles, V. Bonacic-Koutecky, W. von Niessen, A.P. Rendell, V.R. Saunders, and A.J. Stone, GAMESS(UK), CCLRC Daresbury Laboratory, Warrington(1996).
J.S. Craw, J.M. Guest, M.D. Cooper, N.A. Burton, and I.H. Hillier, Effect of hydration on the barrier to internal rotation in formamide. Quantum mechanical calculations including explicit solvent and continuum models, J. Phys. Chem. 100:6304 (1996).
M.D. Cooper, N.A. Burton, R.J. Hall, and I.H, Hillier, Combined Hartree-Fock and density functional theory: A distributed memory parallel implementation, J. Mol. Struct. (Theochem) 315:97 (1994).
W. Smith, and T.R. Forester, DL POLY, CCLRC Daresbury Laboratory, Warrington (1996).
A.J. Robinson, W.G. Richards, P.J. Thomas, and M.M. Hann, Behaviour of cholesterol and its effect on head group and chain conformation in lipid bilayers: A molecular dynamics study, Biophys. J. 68:164(1995).
M. Knaggs, M. Williams, and J.M. Goodfellow, Protein hydration, stability and unfolding, Biochem. Soc. Trans. 711 (1995).
J.M. Goodfellow, M. Knaggs, M. Williams, and J.M. Thornton, Modelling protein unfolding: A solvent insertion protocol, Faraday Discussions 103:339 (1996).
M.A. Williams, J.M. Thornton, and J.M. Goodfellow, Modelling protein unfolding: Hen egg-white lysozyme, Protein Engineer.10:895 (1997).
C.R. Gouldson, C.R. Snell, and C.A. Reynolds, A new approach to docking in the ß2(2)-adrenergic receptor which exploits the domain structure of G-protein coupled receptors, J. Med Chem. 40:3871 (1997).
J. Aqvist, and A. Warshel, Simulation of enzyme reactions using valence-bond force-fields and other hybrid quantum-classical approaches, Chem. Rev. 93:2523 (1993).
U. C. Singh, and P.A. Kollman, A combined ab initio quantum-mechanical and molecular mechanical method for carrying out simulations on complex molecular systems: Application to the CH3CI and Cl− exchange-reaction and gas phase protonation of polyethers, J. Comp. Chem. 7:718 (1986).
M.J. Field, P.A. Bash, and M. Karplus, A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulation, J. Comp. Chem.11:700 (1990).
B. Waszkowycz, I.H. Hillier, N. Gensmantel and D.W. Payling, Aspects of the mechanisms of catalysis in phospholipase A2. A combined ab initio molecular orbital and molecular mechanics study, J. Chem. Soc. Perkin Trans. 2 1795 (1989).
M.J. Harrison, N.A. Burton, and I.H. Hillier, Catalytic mechanism of the enzyme Papain: Predictions using a hybrid quantum mechanical/molecular mechanical potential, J. Amer. Chem. Soc. 119:12285(1997).
A.J. Mulholland, and W.G. Richards, Acetyl-Co A enolization in citrate synthase. A quantum mechanical/molecular mechanical (QM/MM) study, Proteins: Struct. Funct. and Genetics 27:9 (1997).
E.L. Ash, J.L. Sudmeier, E.C. de Fabo, and W.W. Bachovchi, A low-barrier hydrogen bond in the catalytic triad of serine proteases? Theory versus experiment, Science 278:1128 (1997).
A.J. Turner, P. Sherwood, J.A. Barnes, and I.H. Williams, Theoretical modelling of equilibrium isotope effects for the rate-determining step of acid-catalysed hydrolysis of alpha-and beta-methylglucopyranosides: Evaluation of cut-off models and solvation effects using hybrid quantum-mechanical/molecular mechanical methods, in preparation.
A.J. Turner, P. Sherwood, and I.H. Williams, Protium/deuterium fractionation factors for organic molecules in aqueous solution: Calculations using hybrid quantum-mechanical/molecular-mechanical methods, in preparation.
C.F. Rodriquez and I.H. Williams, Mechanism of aldehyde alkylation by dimethylzinc catalysed by a beta-aminoalcohol-zinc complex: A density functional study, in preparation.
J.S. Craw, M.D. Cooper, and I.H. Hillier, The structure and intermolecular interactions of a creatinine designed-receptor complex, studied by ab initio methods, J. Chem. Soc. Perkin Trans. 2 869 (1997).
T.W. Bell, Z. Hou, Y. Luo, M.G.B. Drew, E. Chapoteau, B.P. Czech, and A. Kumar, Detection of creatinine by a designed receptor, Science, 269:671 (1995).
B.R. Smith, M.J. Bearpark, M.A. Robb, F. Bernardi and M. Olivucci, “Classical wavepacket” dynamics through a conical intersection: application to the S1/S0 conical intersection in benzene, Chem. Phys. Lett. 242:27 (1995).
M.J. Bearpark, F. Bernardi, S. Clifford, M. Olivucci, M.A. Robb, B.R. Smith, and T. Vreven, The Azulene S1 state decays via a conical intersection. A CASSCF study with MMVB dynamics, J. Amer. Chem. Soc. 118:169 (1996).
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 1999 Springer Science+Business Media New York
About this chapter
Cite this chapter
Cooper, M.D. et al. (1999). Macromolecular Modelling on the Cray T3D. In: Allan, R.J., Guest, M.F., Simpson, A.D., Henty, D.S., Nicole, D.A. (eds) High-Performance Computing. Springer, Boston, MA. https://doi.org/10.1007/978-1-4615-4873-7_25
Download citation
DOI: https://doi.org/10.1007/978-1-4615-4873-7_25
Publisher Name: Springer, Boston, MA
Print ISBN: 978-1-4613-7211-0
Online ISBN: 978-1-4615-4873-7
eBook Packages: Springer Book Archive