computational chemistry at daresbury 16-22 november 2002 computational science and engineering...

Computational Chemistry at Daresbury 16-22 November 2002

Computational Science and Engineering Department Daresbury Laboratory

Computational Chemistry at Computational Chemistry at Daresbury LaboratoryDaresbury Laboratory

Quantum Chemistry GroupQuantum Chemistry Group

Martyn. F. Guest, Paul. Sherwood and Martyn. F. Guest, Paul. Sherwood and Huub J.J. van Dam Huub J.J. van Dam

http://www.dl.ac.uk/CFShttp://www.dl.ac.uk/CFS

http://www.cse.clrc.ac.uk/Activity/QUASIhttp://www.cse.clrc.ac.uk/Activity/QUASI

Molecular Simulation GroupMolecular Simulation Group

Bill Smith, Maurice Leslie and C.W. YongBill Smith, Maurice Leslie and C.W. Yong

http://www.dl.ac.uk/TCSC/Software/DL_POLYhttp://www.dl.ac.uk/TCSC/Software/DL_POLY



OverviewOverview 1 Activities and Collaborations1 Activities and Collaborations

CCPs (CCP1, CCP5 ..)CCPs (CCP1, CCP5 ..) European collaborations and industrial projectsEuropean collaborations and industrial projects Educational toolsEducational tools

2 Software2 Software Quantum Chemistry - GAMESS-UK, NWChem, CRYSTALQuantum Chemistry - GAMESS-UK, NWChem, CRYSTAL Classical Simulation - DL_POLYClassical Simulation - DL_POLY QM/MM interfaces - ChemShell QM/MM interfaces - ChemShell

3 Methods Developments3 Methods Developments DFT, DRF (Solvation), MR MP2/3, ZORA, DL_POLY developments, DFT, DRF (Solvation), MR MP2/3, ZORA, DL_POLY developments,

QM/MM QM/MM

4 Application Project Areas4 Application Project Areas DFT for Transition Metal complexesDFT for Transition Metal complexes Classical simulation of DNA and Surfactants, powders, molecular crystalsClassical simulation of DNA and Surfactants, powders, molecular crystals QM/MM applications to zeolites, oxide and enzyme catalysisQM/MM applications to zeolites, oxide and enzyme catalysis

5. High-end and Commodity-based systems5. High-end and Commodity-based systems MPP, SMP and Beowulf Parallel Implementations and BenchmarksMPP, SMP and Beowulf Parallel Implementations and Benchmarks



1. Activities and Collaborations1. Activities and Collaborations

Collaborative Computational ProjectsCollaborative Computational Projects CCP1 (Molecular Electronic StructureCCP1 (Molecular Electronic Structure CCP5 (Molecular Simulation)CCP5 (Molecular Simulation)

PNNLPNNL NWChemNWChem

Industrial CollaborationsIndustrial Collaborations Shell, Astra Zeneca, BNFL, UnileverShell, Astra Zeneca, BNFL, Unilever Norsk Hydro, BASF, ICINorsk Hydro, BASF, ICI

European Projects European Projects Quantum Simulation in Industry (QUASI)Quantum Simulation in Industry (QUASI)

Educational SoftwareEducational Software Simulation Java appletSimulation Java applet



CCP1: Molecular Electronic StructureCCP1: Molecular Electronic Structure

Working Group (29 Members from 17 Universities)Working Group (29 Members from 17 Universities) Chaired by Prof P.J. Knowles (University of Birmingham)Chaired by Prof P.J. Knowles (University of Birmingham)

SoftwareSoftware GAMESS-UK, CRYSTAL and ChemShellGAMESS-UK, CRYSTAL and ChemShell

Study Weekends and WorkshopsStudy Weekends and Workshops QM/MM methods (St Andrews, 1995)QM/MM methods (St Andrews, 1995) Quantum Chemistry on MPP Computers (Cambridge, 1995)Quantum Chemistry on MPP Computers (Cambridge, 1995) Quantum Mechanics of Large systems (Daresbury, 1996)Quantum Mechanics of Large systems (Daresbury, 1996) Ab Initio Molecular Dynamics (Daresbury, 1998)Ab Initio Molecular Dynamics (Daresbury, 1998)

Flagship ProjectsFlagship Projects Organic Reactivity (1992-1994), Density Functional Theory (1994-1997)Organic Reactivity (1992-1994), Density Functional Theory (1994-1997) QM/MM Modelling (1997-2001, PDRA: Richard Hall, Manchester.)QM/MM Modelling (1997-2001, PDRA: Richard Hall, Manchester.) Car Parrinello modelling of reactions (2001-2004, Cambridge)Car Parrinello modelling of reactions (2001-2004, Cambridge)

DL Staff SupportDL Staff Support M. F. Guest, P. Sherwood, H.J.J. van Dam, V. R. SaundersM. F. Guest, P. Sherwood, H.J.J. van Dam, V. R. Saunders



CCP5: Molecular SimulationCCP5: Molecular Simulation In existence since 1980. Current theme: Mesoscale simulationIn existence since 1980. Current theme: Mesoscale simulation 688 scientist world-wide are members (265 in UK)688 scientist world-wide are members (265 in UK) Aims:Aims:

Fostering the development of molecular simulation in the UKFostering the development of molecular simulation in the UK Developing software to meet scientific needs and to exploit emergent Developing software to meet scientific needs and to exploit emergent

computer architecturescomputer architectures Provide a forum for contact and information exchange between active Provide a forum for contact and information exchange between active

scientistsscientists ResourcesResources

CCP5 Program Library (~60 programs, including DL_POLY package)CCP5 Program Library (~60 programs, including DL_POLY package) Electronic newsletter and information exchangeElectronic newsletter and information exchange Summer Schools, Software training (DL_POLY)Summer Schools, Software training (DL_POLY) Support staff at Daresbury Laboratory (W. Smith, M. Leslie) Support staff at Daresbury Laboratory (W. Smith, M. Leslie)

http://www.dl.ac.uk/CCP/CCP5http://www.dl.ac.uk/CCP/CCP5



Other CollaborationsOther Collaborations

Related CCP ProjectsRelated CCP Projects CCP2 Atomic and Molecular Physics CCP2 Atomic and Molecular Physics [email protected]@dl.ac.uk CCP3 Surface ScienceCCP3 Surface Science [email protected]@dl.ac.uk CCP6 Heavy Particle DynamicsCCP6 Heavy Particle Dynamics [email protected]@dl.ac.uk UKCP Car ParrinelloUKCP Car Parrinello [email protected]@dl.ac.uk

Pacific Northwest National LabPacific Northwest National Lab NWChem - Massively parallel chemistry software, Global Array toolsNWChem - Massively parallel chemistry software, Global Array tools

IndustryIndustry Shell and Unilever (Zeolite catalysis modelling)Shell and Unilever (Zeolite catalysis modelling) Astra Zeneca (Molecular Crystals)Astra Zeneca (Molecular Crystals) BNFL (Powders, Actinide Chemistry)BNFL (Powders, Actinide Chemistry)

European UnionEuropean Union QUASI (Norsk Hydro/BASF/ICI) QM/MM modellingQUASI (Norsk Hydro/BASF/ICI) QM/MM modelling



Recent MSG CollaborationsRecent MSG Collaborations

RM Lynden-Bel l/P Smith (Belfast) - RM Lynden-Bel l/P Smith (Belfast) - Polymer melts and Polymer melts and DNA+SurfactantDNA+Surfactant

L Woodcock(UMIST)/K Kendal(Birmingham)/C Yong -L Woodcock(UMIST)/K Kendal(Birmingham)/C Yong -Powders Powders friction and flowfriction and flow

M. Lal (Liverpool) - M. Lal (Liverpool) - Au nanoclustersAu nanoclusters J Harding (UCL) - J Harding (UCL) - Grain boundaries/hyperdynamicsGrain boundaries/hyperdynamics N Greaves (Wales) - N Greaves (Wales) - silicate glassessilicate glasses S Melchionna and S Cozzini (Rome) -S Melchionna and S Cozzini (Rome) -DLPROTEINDLPROTEIN Riken Japan - Riken Japan - DL_POLY vector and MDM versionsDL_POLY vector and MDM versions J-C Li/C Burnham (Salford) - J-C Li/C Burnham (Salford) - Structure and dynamics of HStructure and dynamics of H22OO

S. Price (UCL)/Astro-Zeneca(Avecia) - S. Price (UCL)/Astro-Zeneca(Avecia) - Morphology of molecular Morphology of molecular crystalscrystals

S. Parker(Bath) - S. Parker(Bath) - Simulations of minerals under high pressureSimulations of minerals under high pressure



Quantum Simulation in Industry (QUASI)Quantum Simulation in Industry (QUASI) Software DevelopmentSoftware Development

Address barriers to uptake of existing QM/MM methodologyAddress barriers to uptake of existing QM/MM methodology explore range of QM/MM coupling schemesexplore range of QM/MM coupling schemes

– ACA, solid state embeddingACA, solid state embedding dynamics, geometry optimisation for large systemsdynamics, geometry optimisation for large systems maintain flexible approach, address enzymes, zeolites and metal oxide surfacesmaintain flexible approach, address enzymes, zeolites and metal oxide surfaces adopt modular scheme with interfaces to industry standard codesadopt modular scheme with interfaces to industry standard codes

High Performance ComputingHigh Performance Computing Scalable MPP implementationScalable MPP implementation QM/MM MD simulation based on semi-empirical ab-initio and DFT methodsQM/MM MD simulation based on semi-empirical ab-initio and DFT methods

Demonstration ApplicationsDemonstration Applications Value of modelling technology and HPC to industrial problemsValue of modelling technology and HPC to industrial problems Beowulf EV6-based solutionBeowulf EV6-based solution

ExploitationExploitation Disseminate results through workshop, newsletters etc.Disseminate results through workshop, newsletters etc.



QUASI PartnersQUASI Partners

CLRC Daresbury Laboratory (Coordinator)CLRC Daresbury Laboratory (Coordinator) P. Sherwood, M.F. Guest, A.H. de Vries, G. SchreckenbachP. Sherwood, M.F. Guest, A.H. de Vries, G. Schreckenbach

Royal Institution of Great BritainRoyal Institution of Great Britain C.R.A Catlow, A. Sokol, S. French, S BromleyC.R.A Catlow, A. Sokol, S. French, S Bromley

University of Zurich / MPI MulheimUniversity of Zurich / MPI Mulheim W. Thiel, A Turner, S. Billeter, F. Terstegen.W. Thiel, A Turner, S. Billeter, F. Terstegen.

ICI Wilton (UK)ICI Wilton (UK) J. Kendrick (CAPS), S. Rogers (Synetix), J. Casci (Catalco)J. Kendrick (CAPS), S. Rogers (Synetix), J. Casci (Catalco)

Norsk Hydro (Porsgrunn, Norway)Norsk Hydro (Porsgrunn, Norway) K. Schoeffel, O. Swang (SINTEF)K. Schoeffel, O. Swang (SINTEF)

BASF (Ludwigshafen, Germany)BASF (Ludwigshafen, Germany) A. Schaefer, C. LennartzA. Schaefer, C. Lennartz



Educational Software in Computational ScienceEducational Software in Computational Science

Molecular Dynamics: Medium - Web based methodology: HTML, JAVA etc accessible to all standard web browsers.



CCP1 GUI prototypeCCP1 GUI prototype

Functionality (v 0.02)Functionality (v 0.02) - inputs for GAMESS-UK, MOPAC, - inputs for GAMESS-UK, MOPAC,

ChemShellChemShell - coordinate & z-matrix editing- coordinate & z-matrix editing - viewing of orbitals, vibrations, - viewing of orbitals, vibrations,

densitydensity

Uses Python, a concise, open Uses Python, a concise, open source object-oriented languagesource object-oriented language

Designed to run in PyMOL (open Designed to run in PyMOL (open source modelling code) or source modelling code) or standalone.standalone.

Cross-platform (includes Windows, Cross-platform (includes Windows, Linux, Irix, Tru64)Linux, Irix, Tru64)

Requirement is to support a range Requirement is to support a range of CCP1 codesof CCP1 codes Use inheritance from generic Use inheritance from generic

classesclasses ““notebook widget” format, notebook widget” format,

pages can be shared between pages can be shared between codes, easy addition of new codes, easy addition of new pages to customise interfacespages to customise interfaces



2. Software Developments2. Software Developments Generalised Atomic and Molecular Electronic Structure System Generalised Atomic and Molecular Electronic Structure System

(GAMESS-UK)(GAMESS-UK) ab-initioab-initio electronic structure (SCF, DFT, correlated methods) electronic structure (SCF, DFT, correlated methods)

NWChemNWChem Electronic structure & simulation, tools for massively parallel systemsElectronic structure & simulation, tools for massively parallel systems

DL_POLY - GDL_POLY - General MD code (30K atoms)eneral MD code (30K atoms) DL_POLY_3 MD code (~10DL_POLY_3 MD code (~1066 atoms) atoms) DL_DPD dissipative particle dynamics DL_DPD dissipative particle dynamics DL_POLY SDK and Java GUIsDL_POLY SDK and Java GUIs DL_MULTI distributed multipole MD codeDL_MULTI distributed multipole MD code

Static Lattice/DMA CodesStatic Lattice/DMA Codes DMAREL, THBREL - lattice energy minimisationDMAREL, THBREL - lattice energy minimisation

ChemShellChemShell Coupling of applications codes (e.g. GAMESS-UK, DL_POLY)Coupling of applications codes (e.g. GAMESS-UK, DL_POLY) QM/MM methods for solids, surfaces and macromoleculesQM/MM methods for solids, surfaces and macromolecules



2.1 GAMESS-UK2.1 GAMESS-UK

GAMESS-UK is the general purpose ab initio molecular electronic structure GAMESS-UK is the general purpose ab initio molecular electronic structure program for performing SCF-, MCSCF- and DFT-gradient calculations, together program for performing SCF-, MCSCF- and DFT-gradient calculations, together with a variety of techniques for post Hartree Fock calculations.with a variety of techniques for post Hartree Fock calculations.

The program is derived from the original GAMESS code, obtained from Michel The program is derived from the original GAMESS code, obtained from Michel Dupuis in 1981 (then at the National Resource for Computational Chemistry, NRCC), Dupuis in 1981 (then at the National Resource for Computational Chemistry, NRCC), and has been extensively modified and enhanced over the past decade.and has been extensively modified and enhanced over the past decade.

This work has included contributions from numerous authorsThis work has included contributions from numerous authors††, and has been , and has been conducted largely at the CCLRC Daresbury Laboratory, under the auspices of the conducted largely at the CCLRC Daresbury Laboratory, under the auspices of the UK's Collaborative Computational Project No. 1 (CCP1). Other major sources that 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 have assisted in the on-going development and support of the program include various academic funding agencies in the Netherlands, and ICI plc.various academic funding agencies in the Netherlands, and ICI plc.

Additional information on the code may be found from links at:Additional information on the code may be found from links at:http://www.dl.ac.uk/CFShttp://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.



GAMESS-UK features 1.GAMESS-UK features 1. Hartree Fock: Hartree Fock:

Segmented/ GC + spherical harmonic basis sets Segmented/ GC + spherical harmonic basis sets SCF-Energies and Gradients: conventional, in-core, directSCF-Energies and Gradients: conventional, in-core, direct SCF-Frequencies: numerical and analytic 2nd derivatives SCF-Frequencies: numerical and analytic 2nd derivatives Restricted, unrestricted open shell SCF and GVB. Restricted, unrestricted open shell SCF and GVB.

Density Functional Theory Density Functional Theory Energies + gradients, conventional and direct including Dunlap fitEnergies + gradients, conventional and direct including Dunlap fit B3LYP, BLYP, BP86, B97, HCTH, B97-1, FT97 & LDA functionals B3LYP, BLYP, BP86, B97, HCTH, B97-1, FT97 & LDA functionals Numerical 2nd derivatives (analytic implementation in testing) Numerical 2nd derivatives (analytic implementation in testing)

Electron Correlation: Electron Correlation: MP2 energies, gradients and frequencies, Multi-reference MP2, MP3 Energies MP2 energies, gradients and frequencies, Multi-reference MP2, MP3 Energies MCSCF and CASSCF Energies, gradients and numerical 2nd derivatives MCSCF and CASSCF Energies, gradients and numerical 2nd derivatives MR-DCI Energies, properties and transition moments (semi-direct module)MR-DCI Energies, properties and transition moments (semi-direct module) CCSD and CCSD(T) Energies CCSD and CCSD(T) Energies RPA (direct) and MCLR excitation energies / oscillator strengths, RPA gradientsRPA (direct) and MCLR excitation energies / oscillator strengths, RPA gradients Full-CI Energies Full-CI Energies Green's functions calculations of IPs. Green's functions calculations of IPs. Valence bond (Turtle)Valence bond (Turtle)



GAMESS-UK features 2.GAMESS-UK features 2. Molecular Properties: Molecular Properties:

Mulliken and Lowdin population analysis, Electrostatic Potential-Derived Charges Mulliken and Lowdin population analysis, Electrostatic Potential-Derived Charges Distributed Multipole Analysis, Morokuma Analysis, Multipole Moments Distributed Multipole Analysis, Morokuma Analysis, Multipole Moments Natural Bond Orbital (NBO) + Bader Analysis Natural Bond Orbital (NBO) + Bader Analysis IR and Raman Intensities, Polarizabilities & Hyperpolarizabilities IR and Raman Intensities, Polarizabilities & Hyperpolarizabilities Solvation and Embedding Effects (DRF)Solvation and Embedding Effects (DRF) Relativistic Effects (ZORA) Relativistic Effects (ZORA)

Pseudopotentials: Pseudopotentials: Local and non-local ECPs. Local and non-local ECPs.

Visualisation: tools include CCP1 GUIVisualisation: tools include CCP1 GUI Hybrid QM/MM (ChemShell + CHARMM QM/MM) Hybrid QM/MM (ChemShell + CHARMM QM/MM) Semi-empirical : MNDO, AM1, and PM3 hamiltonians Semi-empirical : MNDO, AM1, and PM3 hamiltonians Parallel Capabilities: Parallel Capabilities:

MPP and SMP implementations (GA tools) MPP and SMP implementations (GA tools) SCF/DFT energies, gradients, frequenciesSCF/DFT energies, gradients, frequencies MP2 energies and gradientsMP2 energies and gradients Direct RPA Direct RPA



Parallel Implementation of GAMESS-UKParallel Implementation of GAMESS-UK Early implementation based on message passingEarly implementation based on message passing Subsequent activites under HEC Facilities Agreement with support from Subsequent activites under HEC Facilities Agreement with support from

European projects European projects IMMP (1994-1997, part of EUROPORT)IMMP (1994-1997, part of EUROPORT)

Partners: Guest, Sherwood (Daresbury) - GAMESS-UK, Baerends Partners: Guest, Sherwood (Daresbury) - GAMESS-UK, Baerends (Amsterdam) - ADF, Clark (Erlangen) - VAMP(Amsterdam) - ADF, Clark (Erlangen) - VAMP

Focus on MPP systems (e.g. T3E)Focus on MPP systems (e.g. T3E)Mapping of disk files into global memory (uses GAs)Mapping of disk files into global memory (uses GAs)First MPP MP2 algorithm First MPP MP2 algorithm

– GA storage of transformed integralsGA storage of transformed integrals QUASI (1998-2001)QUASI (1998-2001)

Application of QM/MM methods in IndustryApplication of QM/MM methods in IndustryLed by Daresbury, Partners: Catlow (RI), Thiel (MPI), BASF, ICI, HydroLed by Daresbury, Partners: Catlow (RI), Thiel (MPI), BASF, ICI, HydroFocus on commodity systems, cost-effective computing in industryFocus on commodity systems, cost-effective computing in industry

– demonstrated using Linux alpha commodity cluster at Daresbury.demonstrated using Linux alpha commodity cluster at Daresbury.



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)

2.2 CRYSTAL - Functionality2.2 CRYSTAL - Functionality

Basis SetBasis Set LCAO - GaussiansLCAO - Gaussians All electron or pseudopotentialAll electron or pseudopotential

HamiltonianHamiltonian Hartree-Fock (UHF, RHF)Hartree-Fock (UHF, RHF) DFT (LSDA, GGA)DFT (LSDA, GGA) Hybrid functionalsHybrid functionals

TechniquesTechniques Replicated data parallelReplicated data parallel Distributed data parallelDistributed data parallel

Direct -SCFDirect -SCF VisualisationVisualisation

Cerius2 interfaceCerius2 interface AVS GUI (DLV)AVS GUI (DLV)



Long standing collaboration with Long standing collaboration with HPCC group within EMSLHPCC group within EMSL

ToolsTools Global arrays:Global arrays:

portable distributed data tool:portable distributed data tool:

Used by CCP1 groups (e.g. MOLPRO)Used by CCP1 groups (e.g. MOLPRO)

PeIGS:PeIGS: parallel eigensolver, parallel eigensolver, guaranteed orthogonality guaranteed orthogonality of of

eigenvectorseigenvectors

2.3 Exploiting HPC: The PNNL Collaboration2.3 Exploiting HPC: The PNNL Collaboration NWChemNWChem

Highly efficient and portable MPP Highly efficient and portable MPP computational chemistry packagecomputational chemistry package

Distributed Data - Scalable with Distributed Data - Scalable with respect to chemical system size respect to chemical system size as well as MPP hardware sizeas well as MPP hardware size

Extensible ArchitectureExtensible Architecture Object-oriented designObject-oriented design

– abstraction, data hiding, handles, abstraction, data hiding, handles, APIsAPIs

Parallel programming modelParallel programming model

– non-uniform memory access, non-uniform memory access, global arraysglobal arrays

InfrastructureInfrastructure

– GA, Parallel I/O, RTDB, MA, …GA, Parallel I/O, RTDB, MA, …

Wide range of parallel functionality Wide range of parallel functionality essential for HPCxessential for HPCx

Single, shared data structure

Physically distributed data



High-End Computational ChemistryHigh-End Computational ChemistryThe NWChem SoftwareThe NWChem Software

Capabilities Capabilities (Direct, Semi-direct and conventional):(Direct, Semi-direct and conventional): RHF, UHF, ROHFRHF, UHF, ROHF using up to 10,000 basis functions; analytic 1st using up to 10,000 basis functions; analytic 1st

and 2nd derivatives.and 2nd derivatives. DFTDFT with a wide variety of local and non-local XC potentials, using with a wide variety of local and non-local XC potentials, using

up to 10,000 basis functions; analytic 1st and 2nd derivatives.up to 10,000 basis functions; analytic 1st and 2nd derivatives. CASSCFCASSCF; analytic 1st and numerical 2nd derivatives.; analytic 1st and numerical 2nd derivatives. Semi-direct and RI-based MP2Semi-direct and RI-based MP2 calculations for RHF and UHF wave calculations for RHF and UHF wave

functions using up to 3,000 basis functions; analytic 1st derivatives functions using up to 3,000 basis functions; analytic 1st derivatives and numerical 2nd derivatives.and numerical 2nd derivatives.

Coupled cluster, CCSD and CCSD(T)Coupled cluster, CCSD and CCSD(T) using up to 3,000 basis using up to 3,000 basis functions; numerical 1st and 2nd derivatives of the CC energy. functions; numerical 1st and 2nd derivatives of the CC energy.

Classical molecular dynamics and free energy simulations with the forces obtainable from a variety of sources



2.4 DL_POLY: A Parallel Molecular Dynamics2.4 DL_POLY: A Parallel Molecular Dynamics Simulation Package Simulation Package

First major MD code for parallel platformsFirst 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 1994830 licences issued since 1994 10 industrial licences since 2000.10 industrial licences since 2000. Areas of application:Areas of application:

liquids, solutions, spectroscopy,ionic solids, molecular liquids, solutions, spectroscopy,ionic solids, molecular crystals,polymers,glasses, membranes, proteins, metals, crystals,polymers,glasses, membranes, proteins, metals, solid and liquid interfaces, catalysis, clathrates,liquid solid and liquid interfaces, catalysis, clathrates,liquid crystals, biopolymers, polymer electrolytes.crystals, biopolymers, polymer electrolytes.



Boundary ConditionsBoundary Conditions None (e.g. isolated macromolecules)None (e.g. isolated macromolecules) Cubic periodic boundariesCubic periodic boundaries Orthorhombic periodic boundariesOrthorhombic periodic boundaries Parallelpiped periodic boundariesParallelpiped periodic boundaries Truncated octahedral periodic Truncated octahedral periodic

boundariesboundaries Rhombic dodecahedral periodic Rhombic dodecahedral periodic

boundariesboundaries Slabs (i.e. x,y periodic, z nonperiodic)Slabs (i.e. x,y periodic, z nonperiodic)

Target SystemsTarget Systems Atomic systems & mixtures (Ne, Ar, etc.)Atomic systems & mixtures (Ne, Ar, etc.) Ionic melts & crystals (NaCl, KCl etc.)Ionic melts & crystals (NaCl, KCl etc.) Polarisable ionics (ZSM-5, MgO etc.)Polarisable ionics (ZSM-5, MgO etc.) Molecular liquids & solids (CClMolecular liquids & solids (CCl44, Bz etc.), Bz etc.)

Molecular ionics (KNOMolecular ionics (KNO33, NH, NH44Cl, HCl, H22O etc.)O etc.)

Synthetic polymers ([PhCHCHSynthetic polymers ([PhCHCH22]]nnetc.)etc.) Biopolymers and macromoleculesBiopolymers and macromolecules Polymer electrolytes, Membranes, Polymer electrolytes, Membranes, Aqueous solutions, MetalsAqueous solutions, Metals

MD Algorithms/EnsemblesMD Algorithms/Ensembles

Verlet leapfrog, Verlet leapfrog + RD-SHAKEVerlet leapfrog, Verlet leapfrog + RD-SHAKE Rigid units with FIQA and RD-SHAKERigid units with FIQA and RD-SHAKE Linked rigid units with QSHAKELinked rigid units with QSHAKE Constant T (Berendsen) with Verlet leapfrog Constant T (Berendsen) with Verlet leapfrog

and with RD-SHAKEand with RD-SHAKE Constant T (Evans) with Verlet leapfrog andConstant T (Evans) with Verlet leapfrog and

with RD-SHAKE with RD-SHAKE Constant T (Hoover) with Verlet leapfrogConstant T (Hoover) with Verlet leapfrog

DL_POLY: A Parallel MD Simulation PackageDL_POLY: A Parallel MD Simulation Package



Migration from Replicated to Distributed dataMigration from Replicated to Distributed data DL_POLY-3 : Domain DecompositionDL_POLY-3 : Domain Decomposition

Distribute atoms, forces across the Distribute atoms, forces across the nodesnodes More memory efficient, can address More memory efficient, can address

much larger cases (10 much larger cases (10 55-10 -10 77)) Shake and short-ranges forces require Shake and short-ranges forces require

only neighbour communicationonly neighbour communication communications scale linearly with communications scale linearly with

number of nodesnumber of nodes

Coulombic energy remains globalCoulombic energy remains global strategy depends on problem and strategy depends on problem and

machine characteristicsmachine characteristics Adopt Particle Mesh Ewald scheme

includes Fourier transform smoothed includes Fourier transform smoothed charge density (reciprocal space grid charge density (reciprocal space grid typically 64x64x64 - 128x128x128)typically 64x64x64 - 128x128x128)

AA BB

CC DD



Conventional routines (Conventional routines (e.g.e.g. fftw) assume plane fftw) assume plane or column distributions or column distributions

A global transpose of the data is required to A global transpose of the data is required to complete the 3D FFT and additional costs are complete the 3D FFT and additional costs are incurred re-organising the data from the natural incurred re-organising the data from the natural block domain decomposition. block domain decomposition.

An alternative FFT algorithm has been designed An alternative FFT algorithm has been designed to reduce communication costs. to reduce communication costs.

the 3D FFT are performed as a series of 1D the 3D FFT are performed as a series of 1D FFTs, each involving communications only FFTs, each involving communications only between blocks in a given columnbetween blocks in a given column

More data is transferred, but in far fewer More data is transferred, but in far fewer messagesmessages

Rather than all-to-all, the communications are Rather than all-to-all, the communications are column-wise onlycolumn-wise only

Plane Block

Migration from Replicated to Distributed dataMigration from Replicated to Distributed data DL_POLY-3: Coulomb Energy EvaluationDL_POLY-3: Coulomb Energy Evaluation



2.5 DMAREL: Lattice Simulation2.5 DMAREL: Lattice Simulation

Static lattice energy minimisation of small organic moleculesStatic lattice energy minimisation of small organic molecules Force field anisotropy Force field anisotropy

electrostatic and short rangeelectrostatic and short range Elastic constants and zone centre phonons Elastic constants and zone centre phonons

Free energiesFree energies Symmetry preserved or subgroup selectedSymmetry preserved or subgroup selected Test large number of trial structures for polymorphism -Test large number of trial structures for polymorphism -

Blind test resultsBlind test results

Lommerse JPM, et al. Lommerse JPM, et al. Acta Cryst.Acta Cryst. B 56: 697-714 Part 4 Aug 2000 B 56: 697-714 Part 4 Aug 2000



2.6 ChemShell2.6 ChemShell

A Tcl interpreter for Computational ChemistryA Tcl interpreter for Computational Chemistry Interfaces Interfaces

ab-initio (GAMESS-UK, Gaussian, CADPAC, TURBOMOLE, ab-initio (GAMESS-UK, Gaussian, CADPAC, TURBOMOLE, MOLPRO, NWChem etc)MOLPRO, NWChem etc)

semi-emiprical (MOPAC, MNDO)semi-emiprical (MOPAC, MNDO)MM codes (DL_POLY, CHARMM, GULP)MM codes (DL_POLY, CHARMM, GULP)

optimisation, dynamics (based on DL_POLY routines)optimisation, dynamics (based on DL_POLY routines) utilities (clusters, charge fitting etc)utilities (clusters, charge fitting etc) coupled QM/MM methodscoupled QM/MM methods

Choice of QM and MM codesChoice of QM and MM codesA variety of QM/MM coupling schemesA variety of QM/MM coupling schemes

– electrostatic, polarised, connection atom, Gaussian blur .. electrostatic, polarised, connection atom, Gaussian blur .. QUASI project developments and applications e.g. Organometallics, QUASI project developments and applications e.g. Organometallics,

Enzymes, Oxides, Zeolites Enzymes, Oxides, Zeolites Initial development supported by Shell KSLAInitial development supported by Shell KSLA



3. Methods Developments3. Methods Developments

Ab-initio methodsAb-initio methods DFT ModuleDFT Module DRF Module for Solvation and Embedding DRF Module for Solvation and Embedding Multi-reference MP2/3 and semi-direct Table-CIMulti-reference MP2/3 and semi-direct Table-CI Relativistic ZORA Module Relativistic ZORA Module Interface with CHARMM (c28)Interface with CHARMM (c28)

DL_POLY specialisationDL_POLY specialisation DMA electrostaticsDMA electrostatics Domain DecompositionDomain Decomposition Bio-simulations, hyperdynamics, PIMD, GUIBio-simulations, hyperdynamics, PIMD, GUI

QM/MM MethodsQM/MM Methods Coupling of GAMESS-UK/MNDO/Gaussian with e.g. Coupling of GAMESS-UK/MNDO/Gaussian with e.g.

DL_POLY and GULPDL_POLY and GULP Coupling SchemesCoupling Schemes



3.1 GAMESS-UK Version 6.3 3.1 GAMESS-UK Version 6.3 Gaussian DFT ModuleGaussian DFT Module

Developed by Dr P.E. Young as a modular codeDeveloped by Dr P.E. Young as a modular code interfaced to GAMESS-UKinterfaced to GAMESS-UK

Exchange Correlation Module:Exchange Correlation Module: Supports LDA, B3LYP, BLYP, BP86, BP91, BP97, HCTH, B97-1, FT97Supports LDA, B3LYP, BLYP, BP86, BP91, BP97, HCTH, B97-1, FT97

also made available in the web repositoryalso made available in the web repository Numerical grid-based technology, Radial (Euler Maclaurin, Logarithmic) and Numerical grid-based technology, Radial (Euler Maclaurin, Logarithmic) and

Angular Parts (Gauss Legendre, Lebedev, SG1 grid etc.). Weight schemes Angular Parts (Gauss Legendre, Lebedev, SG1 grid etc.). Weight schemes (Becke, MHL and SSF)(Becke, MHL and SSF)

Extensive use of screening (density matrix and points); scaling O(N1.5) in Extensive use of screening (density matrix and points); scaling O(N1.5) in series of water clustersseries of water clusters

Coulomb ModuleCoulomb Module Dunlap auxiliary Gaussian fitting method (screening on AO shells), semi-direct Dunlap auxiliary Gaussian fitting method (screening on AO shells), semi-direct

option option Multipole developments (stepping stone toward CMM/FMM)Multipole developments (stepping stone toward CMM/FMM)

Coulomb problem split into bi- and mono-electronic region)Coulomb problem split into bi- and mono-electronic region)



DFT QuadratureDFT Quadrature

Logarithmic radial gridLogarithmic radial grid M.E. Mura, P.J. Knowles, J.Chem.Phys. M.E. Mura, P.J. Knowles, J.Chem.Phys. 104104 (1996) 9848 (1996) 9848

Lebedev angular gridLebedev angular grid V.I. Lebedev, Sib.Math.J. V.I. Lebedev, Sib.Math.J. 1818 (1977) 99 (1977) 99

SSF weighting scheme using Murray, Handy, Laming cut-off profilesSSF weighting scheme using Murray, Handy, Laming cut-off profiles R.E. Stratmann, G.E. Scuseria, M.J. Frisch, Chem.Phys.Lett. R.E. Stratmann, G.E. Scuseria, M.J. Frisch, Chem.Phys.Lett. 257257 (1996) 213 (1996) 213 C.W. Murray, N.C. Handy, G.J. Laming, Mol.Phys. C.W. Murray, N.C. Handy, G.J. Laming, Mol.Phys. 7878 (1993) 997 (1993) 997

Murray, Handy, Laming pruning of angular gridMurray, Handy, Laming pruning of angular grid Systematic evaluation of cost/accuracy metricsSystematic evaluation of cost/accuracy metrics

G2 and transition metal test sets (173 molecules)G2 and transition metal test sets (173 molecules) Comparison between implementations: CCP1 code, MOLPRO, and NWChemComparison between implementations: CCP1 code, MOLPRO, and NWChem



Subsequent DFT DevelopmentsSubsequent DFT Developments

Optimisation and parallelisation of coulomb fit codeOptimisation and parallelisation of coulomb fit code library of fitting basis setslibrary of fitting basis sets

Integration with Manchester Gaussian-based softwareIntegration with Manchester Gaussian-based software use of Gaussian charge density expansion for QM/MMuse of Gaussian charge density expansion for QM/MM

Second DerivativesSecond Derivatives Working for RHF and UHF but in need of further optimisationWorking for RHF and UHF but in need of further optimisation Efficiency considerations - AO vs MO basisEfficiency considerations - AO vs MO basis

Partial Hessians and large molecules: AO-basisPartial Hessians and large molecules: AO-basis

– locality of the basis functions allows screening techniques to be locality of the basis functions allows screening techniques to be deployed to maximum effect.deployed to maximum effect.

Small molecules: MO-basisSmall molecules: MO-basis

– only sub-matrices need to be calculated leading to a small only sub-matrices need to be calculated leading to a small prefactor, e.g. occupied-virtual block in CPHF. prefactor, e.g. occupied-virtual block in CPHF.



GAMESS-UK Version 6.3GAMESS-UK Version 6.3 2. Multi-Reference MP2/3 2. Multi-Reference MP2/3

Size consistent, cheap compared to MRCI (MP3 ~ 1 cycle in CI)Size consistent, cheap compared to MRCI (MP3 ~ 1 cycle in CI) Based on perturbation theory with a MC reference functionBased on perturbation theory with a MC reference function

K. Wolinski, H.L. Sellers, P. Pulay, Chem.Phys.Lett. K. Wolinski, H.L. Sellers, P. Pulay, Chem.Phys.Lett. 140140 (1987) 225 (1987) 225 K. Andersson, P-A Malmqvist, B.O. Roos, J.Chem.Phys. K. Andersson, P-A Malmqvist, B.O. Roos, J.Chem.Phys. 9696 (1992) 1218 (1992) 1218 H.-J. Werner, Mol.Phys. H.-J. Werner, Mol.Phys. 8989 (1996) 645 (1996) 645

Implemented as add-on to direct-CI codeImplemented as add-on to direct-CI code H.J.J. van Dam, J.H. van Lenthe, Mol.Phys. H.J.J. van Dam, J.H. van Lenthe, Mol.Phys. 9090 (1997) 1007 (1997) 1007

Involves MCSCF, 4 index, MRMP; most expensive step N Involves MCSCF, 4 index, MRMP; most expensive step N 55

Assigning spectra of OligocyclohexylidenesAssigning spectra of Oligocyclohexylidenes R.W.A. Havenith, H.J.J. van Dam, J.H. van Lenthe, L.W. Jenneskens, Chem.Phys. R.W.A. Havenith, H.J.J. van Dam, J.H. van Lenthe, L.W. Jenneskens, Chem.Phys.

246246 (1999) 49 (1999) 49 The lowest valence transition energies of 1,1’-bicyclohexylidene and 1,1’:4’,1”-The lowest valence transition energies of 1,1’-bicyclohexylidene and 1,1’:4’,1”-

tercyclohexylidenetercyclohexylidene Comparison of MR-MP2, MR-MP3, MRSDCI; MRMP3 ~ MRSDCIComparison of MR-MP2, MR-MP3, MRSDCI; MRMP3 ~ MRSDCI MR-MP3 for the MR-MP3 for the 11BBuu state of 1,1’-bicyclohexylidene took 2.2 hours on a Cray C90, state of 1,1’-bicyclohexylidene took 2.2 hours on a Cray C90,

MRSDCI 7.8 hoursMRSDCI 7.8 hours



GAMESS-UK Version 6.3GAMESS-UK Version 6.33. Relativistic ZORA Module3. Relativistic ZORA Module

ZORA (Zero Order Regular Approximation) is a 2-component alternative ZORA (Zero Order Regular Approximation) is a 2-component alternative to the full 4-component Dirac equation, recovering a large fraction of the to the full 4-component Dirac equation, recovering a large fraction of the relativistic effects.relativistic effects. Ch Chsng, M. Pellisier and Ph. Durand, Phys. Scr. 34 (1986) 394.Ch Chsng, M. Pellisier and Ph. Durand, Phys. Scr. 34 (1986) 394.

Present Implementation includes both 1-component (scalar) and 2-Present Implementation includes both 1-component (scalar) and 2-component treatments (1-electron spin-orbit SCF). component treatments (1-electron spin-orbit SCF). S. Faas, J.G. Snijders, J.H. van Lenthe, E. van Lenthe and E.J. Baerands, S. Faas, J.G. Snijders, J.H. van Lenthe, E. van Lenthe and E.J. Baerands,

Chem. Phys. Letts. 246 (1995) 632.Chem. Phys. Letts. 246 (1995) 632.

ZORA formalism applicable within all the “usual” ab initio techniques ZORA formalism applicable within all the “usual” ab initio techniques (SCF, DFT, CI etc.)(SCF, DFT, CI etc.)

Un-scaled and Scaled ZORA; latter effectively gauge invariantUn-scaled and Scaled ZORA; latter effectively gauge invariant



GAMESS-UK Version 6.3 GAMESS-UK Version 6.3 4. RPA Gradient4. RPA Gradient

Conventional and direct closed shell RPA availableConventional and direct closed shell RPA available C. Fuchs, PhD thesis Freie Universitat Berlin, 1992C. Fuchs, PhD thesis Freie Universitat Berlin, 1992

RPA is a cheap and accurate way to obtain excited states if RPA is a cheap and accurate way to obtain excited states if correlation is similar in ground and excited statecorrelation is similar in ground and excited state J. Pittner, PhD thesis Humbolt Universitaet zu Berlin, 1997J. Pittner, PhD thesis Humbolt Universitaet zu Berlin, 1997

Computing the gradient of an excited stateComputing the gradient of an excited state J.V. Ortiz, J.Chem.Phys. 101(1994) 6743 [errors]J.V. Ortiz, J.Chem.Phys. 101(1994) 6743 [errors] C. van Caillie, R.D. Amos, Chem.Phys.Lett. 308 (1999) 249C. van Caillie, R.D. Amos, Chem.Phys.Lett. 308 (1999) 249

Conventional RPA gradients involve: SCF, 4 index, RPA, HF-gradient, Conventional RPA gradients involve: SCF, 4 index, RPA, HF-gradient, CPHF/Z-vector; costs scale as NCPHF/Z-vector; costs scale as N55

Femto-second dynamics of Sodium Fluorides in the excited state up Femto-second dynamics of Sodium Fluorides in the excited state up to 8 atoms to obtain pump-probe signalsto 8 atoms to obtain pump-probe signals



GAMESS-UK Version 6.3GAMESS-UK Version 6.35. DRF Module for Solvation and Embedding5. DRF Module for Solvation and Embedding

Direct Reaction Field (DRF) model is an embedding technique enabling the Direct Reaction Field (DRF) model is an embedding technique enabling the computation of the interaction of a QM molecule and its classically described computation of the interaction of a QM molecule and its classically described surroundings (University of Groningen, HONDO Implementation)surroundings (University of Groningen, HONDO Implementation) A.H. de Vries, P. Th. Van Duijnen, Int. J. Quant. Chem. 60 (1996) 1111A.H. de Vries, P. Th. Van Duijnen, Int. J. Quant. Chem. 60 (1996) 1111

Modelling of surroundings by four representations that may be freely Modelling of surroundings by four representations that may be freely combined:combined: point charges to model electrostatic field due to surroundingspoint charges to model electrostatic field due to surroundings polarizabilities to model electronic response of surroundingspolarizabilities to model electronic response of surroundings enveloping dielectric to model bulk response (static + electronic)enveloping dielectric to model bulk response (static + electronic) enveloping ionic solution (characterised by Debye screening length)enveloping ionic solution (characterised by Debye screening length)

Embedding may be treated at a number of levels:Embedding may be treated at a number of levels: Electrostatic potential as a perturbation Electrostatic potential as a perturbation Electrostatic potential + reaction field as a perturbationElectrostatic potential + reaction field as a perturbation Treat electrostatic potential self-consistentlyTreat electrostatic potential self-consistently Electrostatic potential self consistently & reaction field as perturbationElectrostatic potential self consistently & reaction field as perturbation Electrostatic potential + reaction field self consistentlyElectrostatic potential + reaction field self consistently



GAMESS-UK Version 6.3 GAMESS-UK Version 6.3 6. QM/MM Interface with CHARMM6. QM/MM Interface with CHARMM

Implemented in collaboration with Bernie Brooks, Eric Billings, (NIH, Implemented in collaboration with Bernie Brooks, Eric Billings, (NIH, Bethesda Maryland)Bethesda Maryland)

Functionality:Functionality: Similar to existing ab-initio interfaces; CHARMM side follows coupling to Similar to existing ab-initio interfaces; CHARMM side follows coupling to

GAMESS(US) (Milan Hodoscek)GAMESS(US) (Milan Hodoscek) Support for Gaussian delocalised point charges implemented in Support for Gaussian delocalised point charges implemented in

GAMESS-UK, based on 2- and 3- centre integral and derivative integral GAMESS-UK, based on 2- and 3- centre integral and derivative integral drivers from the CCP1 DFT module, (Phillip Young).drivers from the CCP1 DFT module, (Phillip Young).

Availability:Availability: CHARMM-capable code incorporated into GAMESS-UK Version 6.2.CHARMM-capable code incorporated into GAMESS-UK Version 6.2. CHARMM (implemented in c26b2 onwards) requires independent CHARMM (implemented in c26b2 onwards) requires independent

licencing from Martin Karplus.licencing from Martin Karplus. Ported to a wide variety of systems including MPPsPorted to a wide variety of systems including MPPs

Origin (Green), Origin (Green), Alphaserver SC (PSC),Alphaserver SC (PSC), Beowulfs ….. Beowulfs …..



Parallel QM/MM Replica PathParallel QM/MM Replica Path

Simultaneous optimisation of Simultaneous optimisation of whole pathwhole path

PMF formalism allows PMF formalism allows reaction energies to be reaction energies to be integrated from forces on integrated from forces on active atoms active atoms less sensitive to less sensitive to

environmental changesenvironmental changes Parallelise each point Parallelise each point

independentlyindependently Provides a scalable Provides a scalable

algorithm for enzyme algorithm for enzyme reactions on MPP reactions on MPP computerscomputers

Non-ReplicatedMM Region

QMRegion

Replicated MMRegion

PP

3366

PP

44PP

3322

PP

33 33

PP

11

PP

00PP

33 44

PP

33 55

PP

33

PP

22

EE

RR ee aa cc tt iioo nn cc oo oo rrdd iinn aa ttee

Application to Chorismate Mutase:Application to Chorismate Mutase: . H.L. . H.L. Woodcock, B.R. Brooks, M. Hodoscek, P. Woodcock, B.R. Brooks, M. Hodoscek, P. Sherwood and Y. S. Lee Sherwood and Y. S. Lee ((Theoretical Chemistry AccountsTheoretical Chemistry Accounts, in press)., in press).



3.2 DL_POLY Current and Future Trends3.2 DL_POLY Current and Future Trends DLPROTEIN: DLPROTEIN:

bio-simulations (developed by University of Rome)bio-simulations (developed by University of Rome) DL_POLY_3: DL_POLY_3:

Domain decomposition version targeted towards million-atom simulations. Domain decomposition version targeted towards million-atom simulations. Applications in biosystems and large scale defects in solids.Applications in biosystems and large scale defects in solids.

DL_POLY_DMA:DL_POLY_DMA: distributed multipoles for accurate modelling of molecular crystals. Applications in distributed multipoles for accurate modelling of molecular crystals. Applications in

drug manufacture.drug manufacture. DL_HYPER:DL_HYPER:

Voter hyperdynamics method for rare event simulation. Applications to diffusion Voter hyperdynamics method for rare event simulation. Applications to diffusion in solids, defect migration etc.in solids, defect migration etc.

DL_PIMD:DL_PIMD: Path integral method to study tunnelling events in low temperature solids. Path integral method to study tunnelling events in low temperature solids.

Applications in glassy systems.Applications in glassy systems. DL_POLY Java GUI.DL_POLY Java GUI.

Universal interface for DL_POLY applications. Universal interface for DL_POLY applications.



3.3 QM/MM Modelling - Challenges3.3 QM/MM Modelling - Challenges Methodological validationMethodological validation

establish reliability of both QM and MM schemesestablish reliability of both QM and MM schemes QM/MM coupling schemes introduce additional artefactsQM/MM coupling schemes introduce additional artefacts consistency of QM and MM energy expressionsconsistency of QM and MM energy expressions

Computational demandsComputational demands macromolecular systems, with extended conformational spacemacromolecular systems, with extended conformational space

conformational search problemsconformational search problems entropic contributionsentropic contributions

QM component means an expensive energy and gradient evaluationQM component means an expensive energy and gradient evaluation Software ComplexitySoftware Complexity

range of forcefield typesrange of forcefield types wide variation in QM and MM program designwide variation in QM and MM program design close integration needed for performance (e.g. HPC), but weak coupling close integration needed for performance (e.g. HPC), but weak coupling

simplifies maintenance (e.g. incorporating new versions of QM and MM simplifies maintenance (e.g. incorporating new versions of QM and MM packages)packages)



QM/MM DevelopmentsQM/MM Developments

Conformational ComplexityConformational Complexity Hybrid Delocalised Internal Coordinates (Thiel/A. Turner/S. Billeter, Zürich, MPI Hybrid Delocalised Internal Coordinates (Thiel/A. Turner/S. Billeter, Zürich, MPI

Mülheim)Mülheim) QM/MM dynamics for molecular and extended systemsQM/MM dynamics for molecular and extended systems

Developments to QM/MM Coupling SchemesDevelopments to QM/MM Coupling Schemes Gaussian Blur (Brooks, NIH)Gaussian Blur (Brooks, NIH) Solid State embedding using shell model and pseudopotentials (Catlow/A. Solid State embedding using shell model and pseudopotentials (Catlow/A.

Sokol, Royal Institution)Sokol, Royal Institution) New InterfacesNew Interfaces

Gaussian, TURBOMOLE etcGaussian, TURBOMOLE etc Graphical Interface for industrial applicationsGraphical Interface for industrial applications

Cerius2 SDKCerius2 SDK



4. Applications Project Areas4. Applications Project Areas

1. Applications of Density Functional Theory1. Applications of Density Functional Theory 1.1 Transition Metals1.1 Transition Metals 1.2 Actinides 1.2 Actinides

2. Classical Simulation2. Classical Simulation 2.1 DNA and Surfactants2.1 DNA and Surfactants 2.2 Modelling of Powder flows2.2 Modelling of Powder flows 2.3 Structural modelling of molecular crystals2.3 Structural modelling of molecular crystals

3. QM/MM Modelling of catalytic systems3. QM/MM Modelling of catalytic systems 3.1 Zeolites3.1 Zeolites 3.2 Enzymes3.2 Enzymes 3.3 Metal Oxide surfaces3.3 Metal Oxide surfaces



4.1.14.1.1 DFT Structures of Transition Metal DFT Structures of Transition Metal ComplexesComplexes

Systematic comparison for 45 TM complexesSystematic comparison for 45 TM complexes RMS deviation between calc/expt bond lengths at HF, MP2 and DFTRMS deviation between calc/expt bond lengths at HF, MP2 and DFT

Basis I (DZ, with 11s8p5d/8s6p2d on TM)Basis I (DZ, with 11s8p5d/8s6p2d on TM) Basis II (DZP, with Wachters 14s11p6d/10s8p3d on TM) . Basis II (DZP, with Wachters 14s11p6d/10s8p3d on TM) .

Satisfactory agreement between each level of theory and experiment Satisfactory agreement between each level of theory and experiment is evident in the transition metal fluorides, chlorides and oxides. is evident in the transition metal fluorides, chlorides and oxides.

Greater discrepancies for CO, hydrides and organometallics:Greater discrepancies for CO, hydrides and organometallics: Hartree Fock exhibits unacceptable errors, with the metal-carbon Hartree Fock exhibits unacceptable errors, with the metal-carbon

distance overestimated in all CO and organometallic complexes.distance overestimated in all CO and organometallic complexes. MP2 typically over compensates for this effect, (especially for M-H bonds, 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.with MP2 leading to bonds lengths too short by some 0.17 A. DFT is more systematic, consistently overestimating experiment by some DFT is more systematic, consistently overestimating experiment by some

0.03-0.05 A (BLYP).0.03-0.05 A (BLYP). Improved distances are given by use of the hybrid schemes (e.g. B3LYP)Improved distances are given by use of the hybrid schemes (e.g. B3LYP)



First-Row Transition Metal-Ligand Bond Lengths (M-L)First-Row Transition Metal-Ligand Bond Lengths (M-L)RMS Deviations from ExperimentRMS Deviations from Experiment

0

0.05

0.1

0.15

0.2

RMS Deviation (B2 basis, Å)

Oxides Fluorides Chlorides Carbonyls Organo-metallics

Hydrides

HFMP2S-VWNB-LYPB3LYPB-P86



Optimised Structures for TM compoundsOptimised Structures for TM compoundsMolecule Point

GroupBLYP HCTH B3LYP B97-1 Expt.

Cr(CO)6 Oh CrCCO

1.9371.164

1.9071.158

1.9291.150

1.9201.151

1.9141.140

Fe(CO)5 D3h FeCax

FeCeq

Coax

COeq

1.8361.8351.1531.166

1.8071.8081.1561.152

1.8331.8251.1481.151

1.8281.8181.1491.151

1.8101.8311.1531.153

Ni(CO)4 Td NiCCO

1.8541.160

1.8391.154

1.8481.146

1.8441.147

1.8381.141

CrO2F2 C2v CrOCrFO-Cr-OF-Cr-F

1.5891.736108.5110.2

1.5661.724108.2110.6

1.5581.717108.3110.2

1.5541.715108.3110.3

1.5751.720107.8111.9

CrO2Cl2 C2v CrOCrClO-Cr-OCl-Cr-Cl

1.5892.157109.4110.9

1.5662.138109.0111.3

1.5592.135109.1111.1

1.5542.131109.1111.2

1.5812.126108.5113.3

Fe(C5H5)2 D5h Fe-CpFeCCCCH

1.6872.0851.4421.0891.1

1.6402.0431.4331.0851.0

1.6882.0801.4291.0821.1

1.6762.0731.4331.0831.2

1.6602.0581.4311.1224.6



4.2 MSG Highlights: 1. Benzene in Silicalite-14.2 MSG Highlights: 1. Benzene in Silicalite-1

Slow diffusion!Slow diffusion! Bluemoon methodBluemoon method Fixed and flexible frameworkFixed and flexible framework Reaction path foundReaction path found Free energy profilesFree energy profiles MC method for DMC method for D00



MSG Highlights: 2. ValinomycinMSG Highlights: 2. Valinomycin

KK++ transport transport in vivoin vivo Studied in model membrane Studied in model membrane

at interfaceat interface KK++ release observed release observed HH22O catalysedO catalysed

K-VM reorientationK-VM reorientation VM restructuringVM restructuring



4.2.14.2.1 DNA and Surfactants DNA and Surfactants In aqueous solution surfactant molecules attach to DNA strandsIn aqueous solution surfactant molecules attach to DNA strands Implication: If DNA can be effectively encapsulated in surfactant it may Implication: If DNA can be effectively encapsulated in surfactant it may

provide a means of transferring DNA fragments through cellular membranes provide a means of transferring DNA fragments through cellular membranes into living cells i.e. gene therapy.into living cells i.e. gene therapy.

What is the nature of this attachment? ExperimentsWhat is the nature of this attachment? Experimentssuggest two possibilities:suggest two possibilities: A surfactant micelle attaches to DNA strandA surfactant micelle attaches to DNA strand Surfactant molecules coat the DNA surfaceSurfactant molecules coat the DNA surface

DL_POLY molecular dynamics simulations haveDL_POLY molecular dynamics simulations have

explored these two possibilities. explored these two possibilities. Collaboration between Universities of Belfast & Collaboration between Universities of Belfast &

Dublin and Daresbury Laboratory.Dublin and Daresbury Laboratory.

Micelle model

`Hairy’ model



DNA and SurfactantsDNA and Surfactants

Large scale simulations of DNA strand (20 Large scale simulations of DNA strand (20 base pairs), Cbase pairs), C1010HH2121-TMA surfactant and -TMA surfactant and

11,000 SPC/E water molecules undertaken.11,000 SPC/E water molecules undertaken. MD simulations show thatMD simulations show that

`Hairy’ model is inherently unstable. `Hairy’ model is inherently unstable. Surfactant molecules either detach or `lie flat’ Surfactant molecules either detach or `lie flat’ on the DNAon the DNA

A surfactant micelle spontaneously attaches A surfactant micelle spontaneously attaches itself to the DNA strand and individual itself to the DNA strand and individual surfactant molecules enter grooves of DNAsurfactant molecules enter grooves of DNA

The micelle model offers a more plausible The micelle model offers a more plausible mechanism for surfactant attachment.mechanism for surfactant attachment.

Experiments are under way to validate these Experiments are under way to validate these conclusions.conclusions.



4.2.24.2.2 Modelling of Powder flows: POWMOD Modelling of Powder flows: POWMOD

POWMOD is a project to investigate the properties of powdersPOWMOD is a project to investigate the properties of powders Topics:Topics:

Microscopic origins of frictionMicroscopic origins of friction Powder compaction and material strengthPowder compaction and material strength Powder flow and associated time dependent phenomenaPowder flow and associated time dependent phenomena

Project commenced October 2000 under EPSRC grantProject commenced October 2000 under EPSRC grant Molecular dynamics methods employed on microscopic and Molecular dynamics methods employed on microscopic and

macroscopic scales.macroscopic scales. Collaborators:Collaborators:

Daresbury LaboratoryDaresbury Laboratory University of BirminghamUniversity of Birmingham UMIST, ManchesterUMIST, Manchester BNFL, CumbriaBNFL, Cumbria

Payoff: better understanding of industrial processesPayoff: better understanding of industrial processes



POWMOD: Friction ModellingPOWMOD: Friction Modelling

MgO probe on MgO surface: Deposition and retraction forcesMgO probe on MgO surface: Deposition and retraction forces



POWMOD: Powder ModellingPOWMOD: Powder Modelling

Physics of powdered materialsPhysics of powdered materials Initial study - friction in ceramic Initial study - friction in ceramic

materialsmaterials Contact forces and hysteresisContact forces and hysteresis Later study - bulk flowsLater study - bulk flows Industrial relevanceIndustrial relevance

MgOMgO



4.2.3 Structure Modelling of Molecular Crystals4.2.3 Structure Modelling of Molecular Crystals

Collaboration between Daresbury Collaboration between Daresbury Laboratory, University College Laboratory, University College London and AstroZenecaLondon and AstroZeneca

Objective: accurate modelling of Objective: accurate modelling of molecular interactions for crystal molecular interactions for crystal structure predictionstructure prediction

Methodology:Methodology: Static lattice methods using Static lattice methods using

THBREL packageTHBREL package Molecular dynamics using Molecular dynamics using

DL_POLYDL_POLY Distributed multipole electrostatic Distributed multipole electrostatic

representationrepresentation Payoff: Production process Payoff: Production process

specification and patentingspecification and patentingmetadinitrobenzene



Molecular Simulation: Future WorkMolecular Simulation: Future Work

HEC - adaptation and extension of software (esp. DL_POLY 3) HEC - adaptation and extension of software (esp. DL_POLY 3) HPCx - code performance optimisation on IBM SP/Regatta-HHPCx - code performance optimisation on IBM SP/Regatta-H DL_HYPER - Hyperdynamics version of DL_POLYDL_HYPER - Hyperdynamics version of DL_POLY Environmental applications of molecular simulation - NERC e-Environmental applications of molecular simulation - NERC e-

Science (M. Dove Cambridge) DL_POLY_3 and large Science (M. Dove Cambridge) DL_POLY_3 and large systems.systems.

Drug preparation and crystal polymorphismDrug preparation and crystal polymorphism CCP5 Renewal 2002-2005 - Mesoscale ModellingCCP5 Renewal 2002-2005 - Mesoscale Modelling Framework 6: Network of Excellence on Nanoscale Framework 6: Network of Excellence on Nanoscale

Technology (CCP5 - based at DL)Technology (CCP5 - based at DL) Biosimulations - possible internal collaboration with SRD on Biosimulations - possible internal collaboration with SRD on

Superoxide dismutases.Superoxide dismutases.



4.3 Modelling of Complex Systems4.3 Modelling of Complex Systems

Electrostatic Fitting ApproachesElectrostatic Fitting Approaches Assume the environment has a fixed geometryAssume the environment has a fixed geometry Use periodic electronic structure and classical codes to provide reference Use periodic electronic structure and classical codes to provide reference

potentialpotential Can relax inner region onlyCan relax inner region only ApplicationsApplications

molecular crystalsmolecular crystalscavities in zeolitescavities in zeolites

QM/MM ModelsQM/MM Models Full Relaxation - Include flexibility (and optionally polarisability) of the Full Relaxation - Include flexibility (and optionally polarisability) of the

environmentenvironment ApplicationsApplications

enzymes, zeolites, organometallics etcenzymes, zeolites, organometallics etc



MolecularCluster

Molecular Potential

Periodic Potential

DifferencePotential

Correction Charges

Fit

Subtract

Periodic Lattice

Proton transfer (ZOH+ + NH3 -> ZO- + NH4+)

S.P. Greatbanks, I.H.Hillier and P. Sherwood, J. Comp. Chem., 18, 562, 1997.Comparison of electrostatic approaches P. Sherwood, A.H. de Vries, S.J. Collins, S.P.Greatbanks, N.A. Burton, M.A. Vincent and I.H. Hillier, Faraday Discuss., 106, 1997

Fitted Charge Models for ZeolitesFitted Charge Models for Zeolites



Coupled QM/MM CalculationsCoupled QM/MM Calculations

To extend application of To extend application of ab-initioab-initio techniques to complex systemstechniques to complex systems Treat reacting core by Quantum Treat reacting core by Quantum

MechanicsMechanics High accuracyHigh accuracy High costHigh cost

Model environment by Molecular Model environment by Molecular MechanicsMechanics

Parameterised force fieldParameterised force field Classical electrostatics Classical electrostatics

QM-MM JunctionQM-MM Junction Link atoms (Link atoms (e.ge.g. H). H) mechanical couplingmechanical coupling polarisation of QM regionpolarisation of QM region



Alkene chemisorptionAlkene chemisorption P.E. Sinclair, A.H. de Vries, P. Sherwood, C.R.A. Catlow and R.A. P.E. Sinclair, A.H. de Vries, P. Sherwood, C.R.A. Catlow and R.A. Van Santen, Van Santen, J. Chem. Soc., Faraday TransJ. Chem. Soc., Faraday Trans., 94, 3401, (1998)., 94, 3401, (1998)

D/H exchange reaction for methaneD/H exchange reaction for methane A.H. de Vries, P. Sherwood, S.J.Collins, A.M. Rigby, A.H. de Vries, P. Sherwood, S.J.Collins, A.M. Rigby, M. Rigutto and G.J. Kramer, M. Rigutto and G.J. Kramer, J. Phys. Chem. BJ. Phys. Chem. B, 103, 6133 (1999), 103, 6133 (1999)

QM/MM Modelling for ZeolitesQM/MM Modelling for Zeolites

Classical - DLPOLY CVFF Classical - DLPOLY CVFF (Hill/Sauer forcefield)(Hill/Sauer forcefield)

Quantum - SCF, DFT (GAMESS-Quantum - SCF, DFT (GAMESS-UK)UK)

Construct finite cluster (termination Construct finite cluster (termination using charge corrections fitted to using charge corrections fitted to Ewald sum)Ewald sum)

QM Model comprises T5 cluster + QM Model comprises T5 cluster + Cu, NO etcCu, NO etc

Electrostatic embeddingElectrostatic embedding



C. Lennartz, A. Schäfer, F. Terstegen, W. Thiel, J. Phys. Chem. B, 2002, 106, 1758-1767.

QUASI Enzyme Application: TIMQUASI Enzyme Application: TIM

Electrostatic embedding (L1 for Electrostatic embedding (L1 for semi-empirical, L2 and charge shift semi-empirical, L2 and charge shift schemes)schemes)

QM: MNDO, TURBOMOLE, MM: QM: MNDO, TURBOMOLE, MM: DL_POLY (CHARMM forcefield)DL_POLY (CHARMM forcefield)

QM/MM cutoffs based on neutral QM/MM cutoffs based on neutral groupsgroups

Termination of QM cluster by Termination of QM cluster by hydrogen atoms.hydrogen atoms.

Comparison of embedding Comparison of embedding schemes and QM methodsschemes and QM methods



QM 1 Int 2 Act 3 Inact 4 BQ 5

Metal Oxide Surface Embedding ModelMetal Oxide Surface Embedding Model

QM: GAMESS-UK, MM: GULPQM: GAMESS-UK, MM: GULP Combined relaxation of shells and Combined relaxation of shells and

electronic degrees of freedomelectronic degrees of freedom Solid-state embedding schemeSolid-state embedding scheme

Finite cluster model, outer sleeve Finite cluster model, outer sleeve of fitted charges charges from 2D of fitted charges charges from 2D Ewald summationEwald summation

Based on ZnO shell model Based on ZnO shell model potentialpotential

Boundary atoms carry both shell Boundary atoms carry both shell model forcefield and model forcefield and pseudopotentialspseudopotentials

QM1 - quantum region, Int2 - interface region, Act3 - Active (relaxed) region, Inact4 - fixed core and shell positions, BQ5 - correcting charges



Modelling methanol synthesis: S.A. French, S.T. Bromley, A.A. Sokol, C.R.A. Catlow, J. Kendrick, S. Rogers, P. Sherwood, Mat. Res. Soc. Symp. Proc., Vol.677, pp AA9.31 AA.9.36, (2001). S.A. French, A.A. Sokol, S. T. Bromley, C.R.A. Catlow, S.C. Rogers, F. King, P. Sherwood., Angew. Chem.-Int. Edit, 2001, 113, p 4437 (2001)

Modelling Methanol Synthesis Modelling Methanol Synthesis Geometry and electronic structure of Geometry and electronic structure of

bulk and surface QM clusters as a bulk and surface QM clusters as a function of cluster size.function of cluster size.

Adsorption of Cu(I) on the ZnO surfaceAdsorption of Cu(I) on the ZnO surface Absorption energies, IR spectra and Absorption energies, IR spectra and

PES for CO on Cu and Zn sitesPES for CO on Cu and Zn sites Stability of Cu clusters of different sizes Stability of Cu clusters of different sizes

and ox. statesand ox. states Structure and energetics of absorption Structure and energetics of absorption

for formate, methoxy and carbonate for formate, methoxy and carbonate Transition states for proton and hydride Transition states for proton and hydride

transfer stepstransfer steps

CO + 2H2 -> CH3(OH)



SummarySummary 1 Activities and Collaborations1 Activities and Collaborations

CCPs (CCP1, CCP5 ..), European collaborations and industrial projectsCCPs (CCP1, CCP5 ..), European collaborations and industrial projects Educational toolsEducational tools

2 Software2 Software Quantum Chemistry (GAMESS-UK, NWChem, CRYSTAL, CPMD)Quantum Chemistry (GAMESS-UK, NWChem, CRYSTAL, CPMD) Classical Simulation - DL_POLY and CharmmClassical Simulation - DL_POLY and Charmm QM/MM interfaces - ChemShell QM/MM interfaces - ChemShell

3 Methods Developments3 Methods Developments DFT, DRF (Solvation), MR MP2/3, ZORA, DL_POLY developments, DFT, DRF (Solvation), MR MP2/3, ZORA, DL_POLY developments,

QM/MM QM/MM

4 Application Project Areas4 Application Project Areas DFT for Transition Metal complexes and actinidesDFT for Transition Metal complexes and actinides Classical simulation of DNA and Surfactants, powders, molecular crystalsClassical simulation of DNA and Surfactants, powders, molecular crystals QM/MM applications to zeolites, oxide and enzyme catalysisQM/MM applications to zeolites, oxide and enzyme catalysis

5. High-end and Commodity-based implementations5. High-end and Commodity-based implementations Parallel and Serial benchmarks Parallel and Serial benchmarks Next presentation …..Next presentation …..

computational chemistry at daresbury 16-22 november 2002 computational science and engineering...

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