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Computational Chemistry at Daresbury Laboratory

Computational Chemistry at Daresbury Laboratory. Quantum Chemistry Group Martyn. F. Guest, Paul. Sherwood and Huub J.J. van Dam http://www.dl.ac.uk/CFS http://www.cse.clrc.ac.uk/Activity/QUASI Molecular Simulation Group Bill Smith, Maurice Leslie and C.W. Yong

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Computational Chemistry at Daresbury Laboratory

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  1. Computational Chemistry at Daresbury Laboratory Quantum Chemistry Group Martyn. F. Guest, Paul. Sherwood and Huub J.J. van Dam http://www.dl.ac.uk/CFS http://www.cse.clrc.ac.uk/Activity/QUASI Molecular Simulation Group Bill Smith, Maurice Leslie and C.W. Yong http://www.dl.ac.uk/TCSC/Software/DL_POLY

  2. Overview • 1 Activities and Collaborations • CCPs (CCP1, CCP5 ..) • European collaborations and industrial projects • Educational tools • 2 Software • Quantum Chemistry - GAMESS-UK, NWChem, CRYSTAL • Classical Simulation - DL_POLY • QM/MM interfaces - ChemShell • 3 Methods Developments • DFT, DRF (Solvation), MR MP2/3, ZORA, DL_POLY developments, QM/MM • 4 Application Project Areas • DFT for Transition Metal complexes • Classical simulation of DNA and Surfactants, powders, molecular crystals • QM/MM applications to zeolites, oxide and enzyme catalysis • 5. High-end and Commodity-based systems • MPP, SMP and Beowulf Parallel Implementations and Benchmarks

  3. 1. Activities and Collaborations • Collaborative Computational Projects • CCP1 (Molecular Electronic Structure • CCP5 (Molecular Simulation) • PNNL • NWChem • Industrial Collaborations • Shell, Astra Zeneca, BNFL, Unilever • Norsk Hydro, BASF, ICI • European Projects • Quantum Simulation in Industry (QUASI) • Educational Software • Simulation Java applet

  4. CCP1: Molecular Electronic Structure • Working Group (29 Members from 17 Universities) • Chaired by Prof P.J. Knowles (University of Birmingham) • Software • GAMESS-UK, CRYSTAL and ChemShell • Study Weekends and Workshops • QM/MM methods (St Andrews, 1995) • Quantum Chemistry on MPP Computers (Cambridge, 1995) • Quantum Mechanics of Large systems (Daresbury, 1996) • Ab Initio Molecular Dynamics (Daresbury, 1998) • Flagship Projects • Organic Reactivity (1992-1994), Density Functional Theory (1994-1997) • QM/MM Modelling (1997-2001, PDRA: Richard Hall, Manchester.) • Car Parrinello modelling of reactions (2001-2004, Cambridge) • DL Staff Support • M. F. Guest, P. Sherwood, H.J.J. van Dam, V. R. Saunders

  5. CCP5: Molecular Simulation • In existence since 1980. Current theme: Mesoscale simulation • 688 scientist world-wide are members (265 in UK) • Aims: • Fostering the development of molecular simulation in the UK • Developing software to meet scientific needs and to exploit emergent computer architectures • Provide a forum for contact and information exchange between active scientists • Resources • CCP5 Program Library (~60 programs, including DL_POLY package) • Electronic newsletter and information exchange • Summer Schools, Software training (DL_POLY) • Support staff at Daresbury Laboratory (W. Smith, M. Leslie) http://www.dl.ac.uk/CCP/CCP5

  6. Other Collaborations • Related CCP Projects • CCP2 Atomic and Molecular Physics c.noble@dl.ac.uk • CCP3 Surface Science a.wander@dl.ac.uk • CCP6 Heavy Particle Dynamics r.j.allan@dl.ac.uk • UKCP Car Parrinello m.plummer@dl.ac.uk • Pacific Northwest National Lab • NWChem - Massively parallel chemistry software, Global Array tools • Industry • Shell and Unilever (Zeolite catalysis modelling) • Astra Zeneca (Molecular Crystals) • BNFL (Powders, Actinide Chemistry) • European Union • QUASI (Norsk Hydro/BASF/ICI) QM/MM modelling

  7. Recent MSG Collaborations • RM Lynden-Bel l/P Smith (Belfast) - Polymer melts and DNA+Surfactant • L Woodcock(UMIST)/K Kendal(Birmingham)/C Yong -Powders friction and flow • M. Lal (Liverpool) - Au nanoclusters • J Harding (UCL) - Grain boundaries/hyperdynamics • N Greaves (Wales) - silicate glasses • S Melchionna and S Cozzini (Rome) -DLPROTEIN • Riken Japan - DL_POLY vector and MDM versions • J-C Li/C Burnham (Salford) - Structure and dynamics of H2O • S. Price (UCL)/Astro-Zeneca(Avecia) - Morphology of molecular crystals • S. Parker(Bath) - Simulations of minerals under high pressure

  8. Quantum Simulation in Industry (QUASI) • Software Development • Address barriers to uptake of existing QM/MM methodology • explore range of QM/MM coupling schemes • ACA, solid state embedding • dynamics, geometry optimisation for large systems • maintain flexible approach, address enzymes, zeolites and metal oxide surfaces • adopt modular scheme with interfaces to industry standard codes • High Performance Computing • Scalable MPP implementation • QM/MM MD simulation based on semi-empirical ab-initio and DFT methods • Demonstration Applications • Value of modelling technology and HPC to industrial problems • Beowulf EV6-based solution • Exploitation • Disseminate results through workshop, newsletters etc.

  9. QUASI Partners • CLRC Daresbury Laboratory (Coordinator) • P. Sherwood, M.F. Guest, A.H. de Vries, G. Schreckenbach • Royal Institution of Great Britain • C.R.A Catlow, A. Sokol, S. French, S Bromley • University of Zurich / MPI Mulheim • W. Thiel, A Turner, S. Billeter, F. Terstegen. • ICI Wilton (UK) • J. Kendrick (CAPS), S. Rogers (Synetix), J. Casci (Catalco) • Norsk Hydro (Porsgrunn, Norway) • K. Schoeffel, O. Swang (SINTEF) • BASF (Ludwigshafen, Germany) • A. Schaefer, C. Lennartz

  10. Educational Software in Computational Science Molecular Dynamics: Medium - Web based methodology: HTML, JAVA etc accessible to all standard web browsers.

  11. Functionality (v 0.02) - inputs for GAMESS-UK, MOPAC, ChemShell - coordinate & z-matrix editing - viewing of orbitals, vibrations, density Uses Python, a concise, open source object-oriented language Designed to run in PyMOL (open source modelling code) or standalone. Cross-platform (includes Windows, Linux, Irix, Tru64) Requirement is to support a range of CCP1 codes Use inheritance from generic classes “notebook widget” format, pages can be shared between codes, easy addition of new pages to customise interfaces CCP1 GUI prototype

  12. 2. Software Developments • Generalised Atomic and Molecular Electronic Structure System (GAMESS-UK) • ab-initio electronic structure (SCF, DFT, correlated methods) • NWChem • Electronic structure & simulation, tools for massively parallel systems • DL_POLY - General MD code (30K atoms) • DL_POLY_3 MD code (~106 atoms) • DL_DPD dissipative particle dynamics • DL_POLY SDK and Java GUIs • DL_MULTI distributed multipole MD code • Static Lattice/DMA Codes • DMAREL, THBREL - lattice energy minimisation • ChemShell • Coupling of applications codes (e.g. GAMESS-UK, DL_POLY) • QM/MM methods for solids, surfaces and macromolecules

  13. 2.1 GAMESS-UK GAMESS-UK is the general purpose ab initio molecular electronic structure program for performing SCF-, MCSCF- and DFT-gradient calculations, together with a variety of techniques for post Hartree Fock calculations. • The program is derived from the original GAMESS code, obtained from Michel Dupuis in 1981 (then at the National Resource for Computational Chemistry, NRCC), and has been extensively modified and enhanced over the past decade. • This work has included contributions from numerous authors†, and has been conducted largely at the CCLRC Daresbury Laboratory, under the auspices of the UK's Collaborative Computational Project No. 1 (CCP1). Other major sources that have assisted in the on-going development and support of the program include various academic funding agencies in the Netherlands, and ICI plc. Additional information on the code may be found from links at: http://www.dl.ac.uk/CFS † M.F. Guest, J.H. van Lenthe, J. Kendrick, K. Schoffel & P. Sherwood, with contributions from R.D. Amos, R.J. Buenker, H.J.J. van Dam, M. Dupuis, N.C. Handy, I.H. Hillier, P.J. Knowles, V. Bonacic-Koutecky, W. von Niessen, R.J. Harrison, A.P. Rendell, V.R. Saunders, A.J. Stone and D. Tozer.

  14. GAMESS-UK features 1. • Hartree Fock: • Segmented/ GC + spherical harmonic basis sets • SCF-Energies and Gradients: conventional, in-core, direct • SCF-Frequencies: numerical and analytic 2nd derivatives • Restricted, unrestricted open shell SCF and GVB. • Density Functional Theory • Energies + gradients, conventional and direct including Dunlap fit • B3LYP, BLYP, BP86, B97, HCTH, B97-1, FT97 & LDA functionals • Numerical 2nd derivatives (analytic implementation in testing) • Electron Correlation: • MP2 energies, gradients and frequencies, Multi-reference MP2, MP3 Energies • MCSCF and CASSCF Energies, gradients and numerical 2nd derivatives • MR-DCI Energies, properties and transition moments (semi-direct module) • CCSD and CCSD(T) Energies • RPA (direct) and MCLR excitation energies / oscillator strengths, RPA gradients • Full-CI Energies • Green's functions calculations of IPs. • Valence bond (Turtle)

  15. GAMESS-UK features 2. • Molecular Properties: • Mulliken and Lowdin population analysis, Electrostatic Potential-Derived Charges • Distributed Multipole Analysis, Morokuma Analysis, Multipole Moments • Natural Bond Orbital (NBO) + Bader Analysis • IR and Raman Intensities, Polarizabilities & Hyperpolarizabilities • Solvation and Embedding Effects (DRF) • Relativistic Effects (ZORA) • Pseudopotentials: • Local and non-local ECPs. • Visualisation: tools include CCP1 GUI • Hybrid QM/MM (ChemShell + CHARMM QM/MM) • Semi-empirical : MNDO, AM1, and PM3 hamiltonians • Parallel Capabilities: • MPP and SMP implementations (GA tools) • SCF/DFT energies, gradients, frequencies • MP2 energies and gradients • Direct RPA

  16. Parallel Implementation of GAMESS-UK • Early implementation based on message passing • Subsequent activites under HEC Facilities Agreement with support from European projects • IMMP (1994-1997, part of EUROPORT) • Partners: Guest, Sherwood (Daresbury) - GAMESS-UK, Baerends (Amsterdam) - ADF, Clark (Erlangen) - VAMP • Focus on MPP systems (e.g. T3E) • Mapping of disk files into global memory (uses GAs) • First MPP MP2 algorithm • GA storage of transformed integrals • QUASI (1998-2001) • Application of QM/MM methods in Industry • Led by Daresbury, Partners: Catlow (RI), Thiel (MPI), BASF, ICI, Hydro • Focus on commodity systems, cost-effective computing in industry • demonstrated using Linux alpha commodity cluster at Daresbury.

  17. 2.2 CRYSTAL - Functionality • Properties • Energy • Structure • Vibrations (phonons) • Elastic tensor • Ferroelectric polarisation • Piezoelectric constants • X-ray structure factors • Density of States / Bands • Charge/Spin Densities • Magnetic Coupling • Electrostatics (V, E, EFG classical) • Fermi contact (NMR) • EMD (Compton, e-2e) • Basis Set • LCAO - Gaussians • All electron or pseudopotential • Hamiltonian • Hartree-Fock (UHF, RHF) • DFT (LSDA, GGA) • Hybrid functionals • Techniques • Replicated data parallel • Distributed data parallel • Direct -SCF • Visualisation • Cerius2 interface • AVS GUI (DLV)

  18. Long standing collaboration with HPCC group within EMSL Tools Global arrays: portable distributed data tool: Used by CCP1 groups (e.g. MOLPRO) PeIGS: parallel eigensolver, guaranteed orthogonality of eigenvectors NWChem Highly efficient and portable MPP computational chemistry package Distributed Data - Scalable with respect to chemical system size as well as MPP hardware size Extensible Architecture Object-oriented design abstraction, data hiding, handles, APIs Parallel programming model non-uniform memory access, global arrays Infrastructure GA, Parallel I/O, RTDB, MA, … Wide range of parallel functionality essential for HPCx 2.3 Exploiting HPC: The PNNL Collaboration Physically distributed data Single, shared data structure

  19. High-End Computational ChemistryThe NWChem Software • Capabilities (Direct, Semi-direct and conventional): • RHF, UHF, ROHF using up to 10,000 basis functions; analytic 1st and 2nd derivatives. • DFT with a wide variety of local and non-local XC potentials, using up to 10,000 basis functions; analytic 1st and 2nd derivatives. • CASSCF; analytic 1st and numerical 2nd derivatives. • Semi-direct and RI-based MP2 calculations for RHF and UHF wave functions using up to 3,000 basis functions; analytic 1st derivatives and numerical 2nd derivatives. • Coupled cluster, CCSD and CCSD(T) using up to 3,000 basis functions; numerical 1st and 2nd derivatives of the CC energy. • Classical molecular dynamicsand free energy simulations with the forces obtainable from a variety of sources

  20. 2.4 DL_POLY: A Parallel Molecular Dynamics Simulation Package • First major MD code for parallel platforms • Developed as CCP5 parallel MD code by W. Smith and T.R. Forester • UK + International user community • 830 licences issued since 1994 • 10 industrial licences since 2000. • Areas of application: • liquids, solutions, spectroscopy,ionic solids, molecular crystals,polymers,glasses, membranes, proteins, metals, solid and liquid interfaces, catalysis, clathrates,liquid crystals, biopolymers, polymer electrolytes.

  21. DL_POLY: A Parallel MD Simulation Package Target Systems • Atomic systems & mixtures (Ne, Ar, etc.) • Ionic melts & crystals (NaCl, KCl etc.) • Polarisable ionics (ZSM-5, MgO etc.) • Molecular liquids & solids (CCl4, Bz etc.) • Molecular ionics (KNO3, NH4Cl, H2O etc.) • Synthetic polymers ([PhCHCH2]netc.) • Biopolymers and macromolecules • Polymer electrolytes, Membranes, • Aqueous solutions, Metals MD Algorithms/Ensembles • Verlet leapfrog, Verlet leapfrog + RD-SHAKE • Rigid units with FIQA and RD-SHAKE • Linked rigid units with QSHAKE • Constant T (Berendsen) with Verlet leapfrog and with RD-SHAKE • Constant T (Evans) with Verlet leapfrog and with RD-SHAKE • Constant T (Hoover) with Verlet leapfrog Boundary Conditions • None (e.g. isolated macromolecules) • Cubic periodic boundaries • Orthorhombic periodic boundaries • Parallelpiped periodic boundaries • Truncated octahedral periodic boundaries • Rhombic dodecahedral periodic boundaries • Slabs (i.e. x,y periodic, z nonperiodic)

  22. B A C D Migration from Replicated to Distributed dataDL_POLY-3 : Domain Decomposition • Distribute atoms, forces across the nodes • More memory efficient, can address much larger cases (10 5-10 7) • Shake and short-ranges forces require only neighbour communication • communications scale linearly with number of nodes • Coulombic energy remains global • strategy depends on problem and machine characteristics • Adopt Particle Mesh Ewald scheme • includes Fourier transform smoothed charge density (reciprocal space grid typically 64x64x64 - 128x128x128)

  23. Conventional routines (e.g. fftw) assume plane or column distributions A global transpose of the data is required to complete the 3D FFT and additional costs are incurred re-organising the data from the natural block domain decomposition. An alternative FFT algorithm has been designed to reduce communication costs. the 3D FFT are performed as a series of 1D FFTs, each involving communications only between blocks in a given column More data is transferred, but in far fewer messages Rather than all-to-all, the communications are column-wise only Migration from Replicated to Distributed dataDL_POLY-3: Coulomb Energy Evaluation Plane Block

  24. 2.5 DMAREL: Lattice Simulation • Static lattice energy minimisation of small organic molecules • Force field anisotropy • electrostatic and short range • Elastic constants and zone centre phonons • Free energies • Symmetry preserved or subgroup selected • Test large number of trial structures for polymorphism - • Blind test results Lommerse JPM, et al. Acta Cryst. B 56: 697-714 Part 4 Aug 2000

  25. 2.6 ChemShell • A Tcl interpreter for Computational Chemistry • Interfaces • ab-initio (GAMESS-UK, Gaussian, CADPAC, TURBOMOLE, MOLPRO, NWChem etc) • semi-emiprical (MOPAC, MNDO) • MM codes (DL_POLY, CHARMM, GULP) • optimisation, dynamics (based on DL_POLY routines) • utilities (clusters, charge fitting etc) • coupled QM/MM methods • Choice of QM and MM codes • A variety of QM/MM coupling schemes • electrostatic, polarised, connection atom, Gaussian blur .. • QUASI project developments and applications e.g. Organometallics, Enzymes, Oxides, Zeolites • Initial development supported by Shell KSLA

  26. 3. Methods Developments • Ab-initio methods • DFT Module • DRF Module for Solvation and Embedding • Multi-reference MP2/3 and semi-direct Table-CI • Relativistic ZORA Module • Interface with CHARMM (c28) • DL_POLY specialisation • DMA electrostatics • Domain Decomposition • Bio-simulations, hyperdynamics, PIMD, GUI • QM/MM Methods • Coupling of GAMESS-UK/MNDO/Gaussian with e.g. DL_POLY and GULP • Coupling Schemes

  27. 3.1 GAMESS-UK Version 6.3 Gaussian DFT Module • Developed by Dr P.E. Young as a modular code • interfaced to GAMESS-UK • Exchange Correlation Module: • Supports LDA, B3LYP, BLYP, BP86, BP91, BP97, HCTH, B97-1, FT97 • also made available in the web repository • Numerical grid-based technology, Radial (Euler Maclaurin, Logarithmic) and Angular Parts (Gauss Legendre, Lebedev, SG1 grid etc.). Weight schemes (Becke, MHL and SSF) • Extensive use of screening (density matrix and points); scaling O(N1.5) in series of water clusters • Coulomb Module • Dunlap auxiliary Gaussian fitting method (screening on AO shells), semi-direct option • Multipole developments (stepping stone toward CMM/FMM) • Coulomb problem split into bi- and mono-electronic region)

  28. DFT Quadrature • Logarithmic radial grid • M.E. Mura, P.J. Knowles, J.Chem.Phys. 104 (1996) 9848 • Lebedev angular grid • V.I. Lebedev, Sib.Math.J. 18 (1977) 99 • SSF weighting scheme using Murray, Handy, Laming cut-off profiles • R.E. Stratmann, G.E. Scuseria, M.J. Frisch, Chem.Phys.Lett. 257 (1996) 213 • C.W. Murray, N.C. Handy, G.J. Laming, Mol.Phys. 78 (1993) 997 • Murray, Handy, Laming pruning of angular grid • Systematic evaluation of cost/accuracy metrics • G2 and transition metal test sets (173 molecules) • Comparison between implementations: CCP1 code, MOLPRO, and NWChem

  29. Subsequent DFT Developments • Optimisation and parallelisation of coulomb fit code • library of fitting basis sets • Integration with Manchester Gaussian-based software • use of Gaussian charge density expansion for QM/MM • Second Derivatives • Working for RHF and UHF but in need of further optimisation • Efficiency considerations - AO vs MO basis • Partial Hessians and large molecules: AO-basis • locality of the basis functions allows screening techniques to be deployed to maximum effect. • Small molecules: MO-basis • only sub-matrices need to be calculated leading to a small prefactor, e.g. occupied-virtual block in CPHF.

  30. GAMESS-UK Version 6.3 2. Multi-Reference MP2/3 • Size consistent, cheap compared to MRCI (MP3 ~ 1 cycle in CI) • Based on perturbation theory with a MC reference function • K. Wolinski, H.L. Sellers, P. Pulay, Chem.Phys.Lett. 140 (1987) 225 • K. Andersson, P-A Malmqvist, B.O. Roos, J.Chem.Phys. 96 (1992) 1218 • H.-J. Werner, Mol.Phys. 89 (1996) 645 • Implemented as add-on to direct-CI code • H.J.J. van Dam, J.H. van Lenthe, Mol.Phys. 90 (1997) 1007 • Involves MCSCF, 4 index, MRMP; most expensive step N 5 • Assigning spectra of Oligocyclohexylidenes • R.W.A. Havenith, H.J.J. van Dam, J.H. van Lenthe, L.W. Jenneskens, Chem.Phys. 246 (1999) 49 • The lowest valence transition energies of 1,1’-bicyclohexylidene and 1,1’:4’,1”-tercyclohexylidene • Comparison of MR-MP2, MR-MP3, MRSDCI; MRMP3 ~ MRSDCI • MR-MP3 for the 1Bu state of 1,1’-bicyclohexylidene took 2.2 hours on a Cray C90, MRSDCI 7.8 hours

  31. GAMESS-UK Version 6.33. Relativistic ZORA Module • ZORA (Zero Order Regular Approximation) is a 2-component alternative to the full 4-component Dirac equation, recovering a large fraction of the relativistic effects. • Ch Chsng, M. Pellisier and Ph. Durand, Phys. Scr. 34 (1986) 394. • Present Implementation includes both 1-component (scalar) and 2-component treatments (1-electron spin-orbit SCF). • S. Faas, J.G. Snijders, J.H. van Lenthe, E. van Lenthe and E.J. Baerands, Chem. Phys. Letts. 246 (1995) 632. • ZORA formalism applicable within all the “usual” ab initio techniques (SCF, DFT, CI etc.) • Un-scaled and Scaled ZORA; latter effectively gauge invariant

  32. GAMESS-UK Version 6.3 4. RPA Gradient • Conventional and direct closed shell RPA available • C. Fuchs, PhD thesis Freie Universitat Berlin, 1992 • RPA is a cheap and accurate way to obtain excited states if correlation is similar in ground and excited state • J. Pittner, PhD thesis Humbolt Universitaet zu Berlin, 1997 • Computing the gradient of an excited state • J.V. Ortiz, J.Chem.Phys. 101(1994) 6743 [errors] • C. van Caillie, R.D. Amos, Chem.Phys.Lett. 308 (1999) 249 • Conventional RPA gradients involve: SCF, 4 index, RPA, HF-gradient, CPHF/Z-vector; costs scale as N5 • Femto-second dynamics of Sodium Fluorides in the excited state up to 8 atoms to obtain pump-probe signals

  33. GAMESS-UK Version 6.35. DRF Module for Solvation and Embedding • Direct Reaction Field (DRF) model is an embedding technique enabling the computation of the interaction of a QM molecule and its classically described surroundings (University of Groningen, HONDO Implementation) • A.H. de Vries, P. Th. Van Duijnen, Int. J. Quant. Chem. 60 (1996) 1111 • Modelling of surroundings by four representations that may be freely combined: • point charges to model electrostatic field due to surroundings • polarizabilities to model electronic response of surroundings • enveloping dielectric to model bulk response (static + electronic) • enveloping ionic solution (characterised by Debye screening length) • Embedding may be treated at a number of levels: • Electrostatic potential as a perturbation • Electrostatic potential + reaction field as a perturbation • Treat electrostatic potential self-consistently • Electrostatic potential self consistently & reaction field as perturbation • Electrostatic potential + reaction field self consistently

  34. GAMESS-UK Version 6.3 6. QM/MM Interface with CHARMM • Implemented in collaboration with Bernie Brooks, Eric Billings, (NIH, Bethesda Maryland) • Functionality: • Similar to existing ab-initio interfaces; CHARMM side follows coupling to GAMESS(US) (Milan Hodoscek) • Support for Gaussian delocalised point charges implemented in GAMESS-UK, based on 2- and 3- centre integral and derivative integral drivers from the CCP1 DFT module, (Phillip Young). • Availability: • CHARMM-capable code incorporated into GAMESS-UK Version 6.2. • CHARMM (implemented in c26b2 onwards) requires independent licencing from Martin Karplus. • Ported to a wide variety of systems including MPPs • Origin (Green), Alphaserver SC (PSC), Beowulfs …..

  35. Non-Replicated MM Region P P P P P P P P P P 0 1 2 3 4 0 1 2 3 4 P P P P P P P P P P Replicated MM 3 2 3 3 3 4 3 5 3 6 3 2 3 3 3 4 3 5 3 6 Region l l l l E E l l l l l l QM Region l l l l R e a c t i o n c o o r d i n a t e R e a c t i o n c o o r d i n a t e Parallel QM/MM Replica Path • Simultaneous optimisation of whole path • PMF formalism allows reaction energies to be integrated from forces on active atoms • less sensitive to environmental changes • Parallelise each point independently • Provides a scalable algorithm for enzyme reactions on MPP computers Application to Chorismate Mutase: . H.L. Woodcock, B.R. Brooks, M. Hodoscek, P. Sherwood and Y. S. Lee (Theoretical Chemistry Accounts, in press).

  36. 3.2 DL_POLY Current and Future Trends • DLPROTEIN: • bio-simulations (developed by University of Rome) • DL_POLY_3: • Domain decomposition version targeted towards million-atom simulations. Applications in biosystems and large scale defects in solids. • DL_POLY_DMA: • distributed multipoles for accurate modelling of molecular crystals. Applications in drug manufacture. • DL_HYPER: • Voter hyperdynamics method for rare event simulation. Applications to diffusion in solids, defect migration etc. • DL_PIMD: • Path integral method to study tunnelling events in low temperature solids. Applications in glassy systems. • DL_POLY Java GUI. • Universal interface for DL_POLY applications.

  37. 3.3 QM/MM Modelling - Challenges • Methodological validation • establish reliability of both QM and MM schemes • QM/MM coupling schemes introduce additional artefacts • consistency of QM and MM energy expressions • Computational demands • macromolecular systems, with extended conformational space • conformational search problems • entropic contributions • QM component means an expensive energy and gradient evaluation • Software Complexity • range of forcefield types • wide variation in QM and MM program design • close integration needed for performance (e.g. HPC), but weak coupling simplifies maintenance (e.g. incorporating new versions of QM and MM packages)

  38. QM/MM Developments • Conformational Complexity • Hybrid Delocalised Internal Coordinates (Thiel/A. Turner/S. Billeter, Zürich, MPI Mülheim) • QM/MM dynamics for molecular and extended systems • Developments to QM/MM Coupling Schemes • Gaussian Blur (Brooks, NIH) • Solid State embedding using shell model and pseudopotentials (Catlow/A. Sokol, Royal Institution) • New Interfaces • Gaussian, TURBOMOLE etc • Graphical Interface for industrial applications • Cerius2 SDK

  39. 4. Applications Project Areas • 1. Applications of Density Functional Theory • 1.1 Transition Metals • 1.2 Actinides • 2. Classical Simulation • 2.1 DNA and Surfactants • 2.2 Modelling of Powder flows • 2.3 Structural modelling of molecular crystals • 3. QM/MM Modelling of catalytic systems • 3.1 Zeolites • 3.2 Enzymes • 3.3 Metal Oxide surfaces

  40. 4.1.1 DFT Structures of Transition Metal Complexes • Systematic comparison for 45 TM complexes • RMS deviation between calc/expt bond lengths at HF, MP2 and DFT • Basis I (DZ, with 11s8p5d/8s6p2d on TM) • Basis II (DZP, with Wachters 14s11p6d/10s8p3d on TM) . • Satisfactory agreement between each level of theory and experiment is evident in the transition metal fluorides, chlorides and oxides. • Greater discrepancies for CO, hydrides and organometallics: • Hartree Fock exhibits unacceptable errors, with the metal-carbon distance overestimated in all CO and organometallic complexes. • MP2 typically over compensates for this effect, (especially for M-H bonds, with MP2 leading to bonds lengths too short by some 0.17 A. • DFT is more systematic, consistently overestimating experiment by some 0.03-0.05 A (BLYP). • Improved distances are given by use of the hybrid schemes (e.g. B3LYP)

  41. First-Row Transition Metal-Ligand Bond Lengths (M-L)RMS Deviations from Experiment HF MP2 S-VWN B-LYP B3LYP B-P86 RMS Deviation (B2 basis, Å) Oxides Fluorides Chlorides Carbonyls Organo- metallics Hydrides

  42. Optimised Structures for TM compounds

  43. 4.2 MSG Highlights: 1. Benzene in Silicalite-1 • Slow diffusion! • Bluemoon method • Fixed and flexible framework • Reaction path found • Free energy profiles • MC method for D0

  44. MSG Highlights: 2. Valinomycin • K+ transport in vivo • Studied in model membrane at interface • K+ release observed • H2O catalysed • K-VM reorientation • VM restructuring

  45. 4.2.1 DNA and Surfactants • In aqueous solution surfactant molecules attach to DNA strands • Implication: If DNA can be effectively encapsulated in surfactant it may provide a means of transferring DNA fragments through cellular membranes into living cells i.e. gene therapy. • What is the nature of this attachment? Experimentssuggest two possibilities: • A surfactant micelle attaches to DNA strand • Surfactant molecules coat the DNA surface • DL_POLY molecular dynamics simulations haveexplored these two possibilities. • Collaboration between Universities of Belfast & Dublin and Daresbury Laboratory. Micelle model `Hairy’ model

  46. DNA and Surfactants • Large scale simulations of DNA strand (20 base pairs), C10H21-TMA surfactant and 11,000 SPC/E water molecules undertaken. • MD simulations show that • `Hairy’ model is inherently unstable. Surfactant molecules either detach or `lie flat’ on the DNA • A surfactant micelle spontaneously attaches itself to the DNA strand and individual surfactant molecules enter grooves of DNA • The micelle model offers a more plausible mechanism for surfactant attachment. • Experiments are under way to validate these conclusions.

  47. 4.2.2 Modelling of Powder flows: POWMOD • POWMOD is a project to investigate the properties of powders • Topics: • Microscopic origins of friction • Powder compaction and material strength • Powder flow and associated time dependent phenomena • Project commenced October 2000 under EPSRC grant • Molecular dynamics methods employed on microscopic and macroscopic scales. • Collaborators: Daresbury Laboratory • University of Birmingham • UMIST, Manchester • BNFL, Cumbria • Payoff: better understanding of industrial processes

  48. POWMOD: Friction Modelling • MgO probe on MgO surface: Deposition and retraction forces

  49. POWMOD: Powder Modelling • Physics of powdered materials • Initial study - friction in ceramic materials • Contact forces and hysteresis • Later study - bulk flows • Industrial relevance MgO

  50. 4.2.3 Structure Modelling of Molecular Crystals • Collaboration between Daresbury Laboratory, University College London and AstroZeneca • Objective: accurate modelling of molecular interactions for crystal structure prediction • Methodology: • Static lattice methods using THBREL package • Molecular dynamics using DL_POLY • Distributed multipole electrostatic representation • Payoff: Production process specification and patenting metadinitrobenzene

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