Materials Simulation Center presents:

Introduction to Computational Chemistry Programs

Ping Lin

Course contents
Overview: O i Wh What t is i Computational C t ti l Chemistry Ch i t 1: ab initio method 2: Density Functional Theory 3: Molecular mechanics method 4: Introduction to some programs

Introduction to Computational Chemistry

Overview: What is Computational Chemistry

Computational Chemistry uses the results of theoretical chemistry, incorporated into efficient computer programs, to calculate the structures and properties of molecules and solids. Computational chemistry methods range from highly accurate (i.e. Ab initio methods and DFT) to less accurate, (i.e. semiempirical method), to very approximate (i.e. Molecular Mechanics Coarse Mechanics, Coarse-Grain Grain model). model) It can deal with system of a single molecule, a group of molecules, a liquid or solid. It calculates properties such as properties are structure, relative energies, charge distributions, dipoles and multipole moments, vibrational frequencies frequencies, reactivity and other spectroscopic quantities, etc.

Introduction to Computational Chemistry

Simulation method for length and time scale

TIME /s
100
3 (ms) 10-3

Continuum M th d Methods

Atomistic Si l ti Simulation Methods

Mesoscale methods
Lattice Monte Carlo Brownian dynamics Dissipative particle dyn

(s) 10-6

9 (ns) 10-9

Semi-empirical methods Ab initio methods

Monte Carlo molecular dynamics

(ps) 10-12

(fs)

10-15

tight-binding MNDO, INDO/S

10-10

10-9

(nm)

10-8

10-7

(m)

10-6

10-5

10-4

LENGTH /meters

Figure 1. Schematic illustration of the simulation methods for different length and time scales
Introduction to Computational Chemistry

Methods
Ab initio i iti quantum t chemistry h i t methods th d Density functional theory (DFT) methods Semi-empirical quantum chemistry method Molecular mechanics method Specially treatment for periodic boundary condition
Plane waves implementation Ewald summation for long-range interaction

Molecular dynamics and Monte Carlo simulation Hybrid quantum mechanics/molecular mechanics method
Introduction to Computational Chemistry

Ab initio quantum chemistry methods

Ab initio quantum chemistry solves electronic Schrdinger equation from mathematical principles. The term ab initio indicates that the calculation is derived from first principles and does not rely on any empirical ii ld data. t

Introduction to Computational Chemistry

Commonly used methods

Hartree-Fock methods
o o o Hartree-Fock (HF) Restricted Open-shell Hartree-Fock (ROHF) Unrestricted Hartree-Fock (UHF) Mller Plesset perturbation theory (MPn) Mller-Plesset Configuration interaction (CI) Coupled cluster (CC) Quadratic configuration interaction (QCI) Q Quantum t chemistry h i t composite it methods th d (G1 (G1, G2, G2 CBS)

Post-Hartree-Fock methods
o o o o o

Multi-reference methods
o o o Multi-configurational self-consistent field (MCSCF) Multi-reference configuration interaction (MRCI) Complete Active Space Perturbation Theory (CASPTn)

Introduction to Computational Chemistry

Electron atomic and molecular orbitals

HOMO

LUMO

HOMO-1

LUMO+1

HOMO-2

LUMO+2

HOMO-3

LUMO 3 LUMO+3

HOMO-4

LUMO+4

Introduction to Computational Chemistry

Molecular Orbital Theory & Hartree-Fock Method

Total wave function as a Slater Determinant

1 (1) 2 (1) 1 1 (2) 2 (2) = L N! L 1 ( N) 2 ( N)

L N (1) L N ( 2) L L

i = ci
=1

L N ( N)

LCAO: Linear Combination of Atomic Orbitals

i = ci
=1

Variation Principle

Hartree-Fock (HF)

Introduction to Computational Chemistry

Post-Hartree-Fock Method

Introduction to Computational Chemistry

Basis Set
STO

i = ci
=1

GTO

r Minimal basis sets: STO-3G Split-valence basis sets: 3-21G, 6-31G Polarisation functions are denoted with * (3-21G*, 6-31G*) Diffuse Diff f functions ti are denoted d t db by + (6 (6-31+G*) 31 G*) * The selection of basis set is a key factor to the accuracy of the numeric solution.

Introduction to Computational Chemistry

Level of Theory

Introduction to Computational Chemistry

Cost vs. Accuracy

Introduction to Computational Chemistry

Methods
Ab initio i iti quantum t chemistry h i t methods th d Density functional theory (DFT) methods Semi-empirical quantum chemistry method Molecular mechanics method Specially treatment for periodic boundary condition
Plane waves implementation Ewald summation for long-range interaction

Molecular dynamics and Monte Carlo simulation Hybrid quantum mechanics/molecular mechanics method
Introduction to Computational Chemistry

Density functional theory methods

Hohenberg-Kohn Hohenberg Kohn Theorem (1964) All properties of the many-body system are determined by the ground state density n0(r) Each property is a functional of the ground state density n0(r) which is written as f [n0] A functional f [n0] maps a function to a result: n0(r) f Kohn-Sham ansatz (1965) Replace original many-body problem with an independent electron problem bl that th t can be b solved! l d! The ground state density is required to be the same as the exact density
Introduction to Computational Chemistry

Exchange-Correlation Functional

Local Density Approximation - LDA

Exc can be determined using homogeneous electron gas model or using quantum Monte Carlo methods

Gradient approximations - GGA

Introduction to Computational Chemistry

Correlation-Exchange Functional
VWN5 BLYP HCTH BP86
Increasing qualit ty and com mputationa al cost

LDA local density GGA gradient corrected Meta-GGA M t GGA kinetic energy density included Hybrid exact HF exchange component Hybrid-meta-GGA

TPSS M06-L B3LYP B97/2 MPW1K

MPWB1K M06

Introduction to Computational Chemistry

Software supporting DFT

[Link]
Introduction to Computational Chemistry

Methods
Ab initio i iti quantum t chemistry h i t methods th d Density functional theory (DFT) methods Semi-empirical quantum chemistry method Molecular mechanics method Specially treatment for periodic boundary condition
Plane waves implementation Ewald summation for long-range interaction

Molecular dynamics and Monte Carlo simulation Hybrid quantum mechanics/molecular mechanics method
Introduction to Computational Chemistry

Semi-empirical quantum chemistry method

CNDO (1965, Pople et al) MINDO (1975, Dewar ) MNDO (1977, Thiel) Thiel) INDO (1967, Pople et al) ZINDO SINDO1

STOSTO -basis (/S (/S-spectra,/2 d d-orbitals) orbitals) /1/2/3, organics /d, organics, transition metals O Organics i Electronic spectra, transition metals 1-3 row binding energies, photochemistry and transition metals

Introduction to Computational Chemistry

Further improvement

AM1

Modified nuclear repulsion terms model to account for H-bonding (1985 (1985, Dewar et al) Widely used today (transition metals, inorganics inorganics) )

PM3 (1989, Stewart)

Larger data set for parameterization compared to AM1 Widely used today (transition metals, inorganics inorganics) )

Introduction to Computational Chemistry

Methods
Ab initio i iti quantum t chemistry h i t methods th d Density functional theory (DFT) methods Semi-empirical quantum chemistry method Molecular mechanics method Specially treatment for periodic boundary condition
Plane waves implementation Ewald summation for long-range interaction

Molecular dynamics and Monte Carlo simulation Hybrid quantum mechanics/molecular mechanics method
Introduction to Computational Chemistry

Molecular mechanics method

Interactions between atoms (Potential Energy Function) are represented by functions of distance, angle or dihedral Collection of empirical parameters and potential functions is known as a force field. i.e. AMBER force field:

Introduction to Computational Chemistry

Commonly used force field

Amber OPLS CHARMM GROMOS Dreiding MM2/MM3 Water DNA, proteins and lipids. Generalized Amber Force Field (GAFF) covers most organic space. Organic molecules in the liquid phase. Available as all-atom (AA) or united-atom (UA) form. DNA, proteins, lipids, sugars. General purpose. Organic and biochemical space. General purpose. Includes some parameters for metals and main group elements. General purpose. MM2 used for hydrocarbons. MM3 includes most of organic space plus some other main g group p and metal atom types. yp Rigid and flexible models available. TIP3P widely used in biological simulation.

Introduction to Computational Chemistry

Commonly used softwares

Introduction to Computational Chemistry

Common tasks
Sampling conformational spaces (Structure and dynamics) Free energy calculation (Binding energy) Structural refinement (based on NMR data) Reaction path (Transition Path Sampling) Molecular interaction (Ligand-Protein) ( g ) Investigate mutational effects etc. t

Introduction to Computational Chemistry

Applications
Speed of method opens up a wide range of systems Amorphous condensed phase liquids, liquid crystals, glasses Biological systems Biopolymers, membranes Nanotubes and molecular machines

Fast calculations allow large numbers of conformers to be screened Drug docking analysis Global minimum searches

Statistical data can be collected Access to bulk properties (via statistical mechanics) Simulation of finite temperature behaviour and phase changes

Introduction to Computational Chemistry

Methods
Ab initio i iti quantum t chemistry h i t methods th d Density functional theory (DFT) methods Semi-empirical quantum chemistry method Molecular mechanics method Specially treatment for periodic boundary condition
Periodic Electronic Structure Calculations Ewald summation for long-range interaction

Molecular dynamics and Monte Carlo simulation Hybrid quantum mechanics/molecular mechanics method
Introduction to Computational Chemistry

Systems with periodic boundary condition

0 to 3 Dimension system (3D (condense phase) phase), 2D (surfaces) (surfaces), 1D (polymers) and 0D (molecule))

Introduction to Computational Chemistry

Blochs Theorem
The electronic Th l t i wave function f ti i in a periodic i di potential t ti l expressed as

nk

(r ) can b be

nk k

( r ) = k c ik exp p ( ik .r )

nk

(r )

k is wavevector within the first Brillouin zone

Introduction to Computational Chemistry

Plane wave and pseudopotential

Plane wave b Pl basis i set t is i a natural t l choice h i f for th the periodic i di electronic wave function due to its periodicity and its mathematical and computational convenience.

i (r ) = k cik exp (ik .r )

Application of pseudopotential can effectively: reduce the size of basis set ; reduce the size of the system (less electrons) take into account of the relativistic and other effects

Introduction to Computational Chemistry

Long-range interaction in Molecular Mechanics

Ewald summation Fast Multipole Method Particle Mesh Ewald Multi-grid summation

O(N 3/2 ) O(N) O(N ( log g N) ) O(N)

Ewald, 1921 Greengard, 1987 Darden, , 1993 Brandt et al., 1990 Skeel et al., 2002 Izaguirre et al., 2003

Introduction to Computational Chemistry

Computational Chemistry Codes on Clusters

Quantum Chemistry package for molecular systems
GAMESS GAUSSIAN Jaguar NWCHEM ORCA QCHEM SPARTAN TURBOMOLE

Quantum chemistry package for solids/surface

ABINIT CPMD CASTEP NWCHEM VASP

Molecular Mechanics Packages g

AMBER CHARMM DL_POLY GROMACS LAMMPS NAMD Molden y Pymol Rosetta XPLOR

Others

3D-DOCK AUTODOCK HADDOCK

VMD

Introduction to Computational Chemistry

Molecular Quantum Chemistry Packages

Introduction to Computational Chemistry

Quantum Chemistry package on clusters

GAMESS (US) GAUSSIAN NWCHEM ORCA QCHEM SPARTAN TURBOMOLE

Introduction to Computational Chemistry

GAMESS
General Atomic and Molecular Electronic Structure System Primary focus is on ab initio quantum chemistry calculations Also includes DFT, , semi-empirical p ( (AM1, , PM3) ) and QM/MM capabilities

Early version of GAMESS is available under /usr/global/gamess scripts need to execute the program

Introduction to Computational Chemistry

GAMESS Input file

! $CONTRL SCFTYP=RHF RUNTYP=OPTIMIZE COORD=CART NZVAR=0 MULT=1 ICHARG=0 $END $SYSTEM TIMLIM=20000 MEMORY=10000000 $ $ $END $STATPT NSTEP=1000 $END $BASIS GBASIS=STO NGAUSS=3 $END $GUESS GUESS=HUCKEL $END $DATA Test...HCHO molecule - RHF/STO-3G (a comment line) Cn 1 C O H H $END 6.0 8.0 1.0 1.0 0.6084782705 -0.6082418894 1.2040919862 1.2040973125 -0.0000011694 -0.0000002093 -0.9264398115 0.9264340484 0.000000000000 0.000000000000 0.000000000000 0.00000000000

Introduction to Computational Chemistry

GAUSSIAN
Gaussian 03 is a general electronic structure programs. Gaussian 03 is used by chemists, chemical engineers, biochemists, physicists and others for research in established and emerging areas of chemical i t interest. t

Introduction to Computational Chemistry

Gaussian Input File Structures

Link 0 Commands (% lines): System specific parameter Route section (# lines): Specify calculation type, model chemistry and other options Title section: Brief description of the calculation Molecule specification: Specify molecular system to be studied Optional additional sections: Additional input needed for specific job types
%NProcShared=2 %MEM 64MW %MEM=64MW %chk=h2o_opt.chk # RHF/6-31g** OPT H2O RHF/6 RHF/6-31g** 31 ** optimization ti i ti 0 1 O H 1 r1 1 H 1 r1 2 tha1 r1 1.000 th 1 105 tha1 105.0 0 Introduction to Computational Chemistry Link 0 section (#of processors for SMP) (amount of memory) (checkpoint file name and location) Route section Title section Molecule Specification section (charge, multiplicity) Structure representation in Z-matrix format

Route Section: Keywords

# ADMP AM1 Amber Archive B3LYP BD BOMD CASSCF CBS Keywords CBSExtrapolate CCD Charge ChkBasis CID CIS CNDO Complex Constants Counterpoise CPHF Density DensityFit Dreiding ExtendedHuckel External ExtraBasis Frozen Core Options Field FMM Force Frequency G* Keywords G Gen Geom GFInput GFPrint G Guess GVB Hartree-Fock Huckel INDO Integral IOp IRC IRCMax LSDA MaxDisk MINDO3 MM MNDO MP* Keywords Name NMR ONIOM Opt Output OVGF PBC PM3 P l Polar Population Pressure Prop Pseudo Punch QCISD ReArchive SAC-CI Scale Scan SCF SCRF SP Sparse Stable Symmetry TD Temperature Test TestMO TrackIO Transformation UFF Units Volume W1U Zindo Link 0 Commands Non-Standard Routes Program Development Keywords Density Functional Methods

Introduction to Computational Chemistry

Keywords (Job types)

SP Opt Freq IRC Scan Polar Force Volume Si l point Single i energy. Geometry optimization. Frequency and thermochemical analysis. Reaction path following. Find the maximum energy along a specific reaction path. Potential energy gy surface scan. Polarizabilities and hyperpolarizabilities. Direct dynamics trajectory calculation. Compute forces on the nuclei nuclei. Compute molecular volume.

IRCMax

ADMP and BOMD

Introduction to Computational Chemistry

Keywords (Molecular properties)

o Atomic charges charges, Dipole moment moment, Multipole moments : Pop o Electron affinities and Ionization potentials via propagator methods: OVGF o Electron density: cubegen o Electronic circular dichroism: TD o Electrostatic potential: cubegen, Prop o Electrostatic-potential derived charges: Pop=Chelp, ChelpG or MK o Frequency-dependent polarizabilities/hyperpolarizabilities: Polar CPHF=RdFreq o High accuracy energies: CBS-QB3, G2, G3, W1U o Hyperfine coupling constants (anisotropic): Prop o Hyperfine spectra tensors (incl. g tensors): Freq=(VCD, VibRot[, Anharmonic]) o Hyperpolarizabilities: Freq, Polar o IR and Raman spectra: Freq o Molecular orbitals: Pop Pop=Regular Regular o NMR shielding and chemical shifts: NMR o NMR spin-spin coupling constants: NMR=SpinSpin o Optical rotations: Polar=OptRot CPHF=RdFreq o Polarizabilities: Freq, Polar o Thermochemical analysis: Freq o UV/Visible spectra: CIS, Zindo, TD o Vibration-rotation coupling: Freq=VibRot o Vibrational circular dichroism: Freq Freq=VCD VCD Introduction to Computational Chemistry

Available model calculations

Introduction to Computational Chemistry

Keyword (Basis set)

Basis Set STO-3G 3-21G 6-21G 4-31G 6-31G , 6-311G D95 D95V SHC CEP-4G , CEP-31G, CEP121G LanL2MB LanL2DZ SDD, SDDAll cc-pV(DTQ5)Z cc-pV6Z SV , SVP TZV and TZVP MidiX EPR-II EPR-III EPR-II, UGBS MTSmall DGDZVP DGDZVP2 DGTZVP Applies to H-Xe H-Xe H-Cl H-Ne H-Kr H-Cl except Na and Mg H-Ne H-Cl H-Rn H-Ba, H Ba, La La-Bi Bi H, Li-Ba, La-Bi all but Fr and Ra H-He, B-Ne, Al-Ar, Ga-Kr H B-Ne H, H-Kr H-Kr H, C-F, S-Cl, I, Br H B H, B, C C, N N, O O, F H-Lr H-Ar H-Xe H-F, Al-Ar, Sc-Zn H, C-F, Al-Ar included in definition included in definition in SVP included in definition included in definition included in definition UGBS(1,2,3)P added via AUG- prefix added via AUG- prefix Polarization Functions * * or ** (d) (d) or (d,p) (3df,3pd) (3df,3pd) (d) or (d,p) * * (Li-Ar only) Diffuse Functions +

++ ++ ++

Introduction to Computational Chemistry

Molecular Specification
Molecules can be specified by ZZ matrix or Cartesian coordinate. The Z-matrix is a way to represent a system t built b ilt of f atoms. t It provides id a description of each atom in a molecule in terms of its atomic number, bond length bond angle length, angle, and dihedral angle, the so-called internal coordinates.
Molecular builders Some softwares provide sketcher and fragment library to build molecules with ease i ease, i.e. e GaussView GaussView, Accerlyss Accerlys s Discovery Studio Studio, Materials Studio Studio, Java Molecular Editor, HyperChem, Gabedit, etc. Some softwares provide interface to write out z-matrix or Cartesian coordinates, i.e. Molden
Introduction to Computational Chemistry

NWCHEM
NWChem is a computational chemistry package with many capabilities, including: Molecular electronic structure calculations Pseudopotential plane-wave electronic structure calaculations Ab intio and classical molecular dynamics and more

Introduction to Computational Chemistry

NWCHEM Input file format

start t t water t Title H2o energy geometry units au
O H H 0.00000 0.00000 0.00000 0.000000 1.43042809 -1.43042809 0.000000 -1.10715266 1.10715266 -1.10715266

End Basis * library 3-21G End MP2; freeze atomic; END Task mp2 energy

Job name determines names for temporary files <module> end blocks change settings for future calculations task directive triggers calculation input is handled strictly top top-toto input bottom (only settings above a task have an impact) Python procedures for more complicated structures

Introduction to Computational Chemistry

Quantum chemistry package for solids/surface

ABINIT ADF/Band CPMD CASTEP NWCHEM VASP

Introduction to Computational Chemistry

VASP (Vienna Ab-initio Simulation Package)

VASP is a complex package for performing ab-initio quantum-mechanical molecular dynamics (MD) simulations using pseudopotentials or the projector-augmented wave method and a plane wave basis set. The approach implemented in VASP is based on the (finitetemperature) local-density approximation with the free energy as variational quantity and an exact evaluation of the instantaneous electronic ground state at each MD time step. VASP uses efficient matrix diagonalisation schemes and an efficient Pulay/Broyden charge d density it mixing. i i The interaction between ions and electrons is described by ultra-soft Vanderbilt pseudopotentials (US-PP) or by the projector-augmented wave (PAW) method. th d Forces and the full stress tensor can be calculated with VASP and used to relax atoms into their instantaneous ground-state.
Introduction to Computational Chemistry

VASP Input
INPUT Files POSCAR POTCAR KPOINTS INCAR OUPUT Files OUTCAR OSZICAR CONTCAR CHGCAR WAVECAR EIGENVAL PROCAR XDATCAR LOCPOT DOSCAR CHG

STOPCAR is used to signal stopping VASP execution

Introduction to Computational Chemistry

Structure Input File

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Pseudopotential File

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KPOINT Sampling

Introduction to Computational Chemistry

CONTROL File

Introduction to Computational Chemistry

Result analysis

Introduction to Computational Chemistry

CPMD
The CPMD code Th d is i a plane l wave/pseudopotential / d t ti l implementation i l t ti of f Density Functional Theory, particularly designed for ab-initio molecular dynamics.
isolated systems and system with periodic boundary conditions; k-points molecular and crystal symmetry wavefunction optimization: direct minimization and diagonalization geometry optimization: local optimization and simulated annealing molecular dynamics: constant energy, constant temperature and constant pressure path integral MD response functions excited it d states t t many electronic properties time-dependent DFT (excitations, molecular dynamics in excited states)

Introduction to Computational Chemistry

CPMD Input file 1 (Wave Function)

&CPMD OPTIMIZE WAVEFUNCTION CONVERGENCE ORBITALS 1.0e-8 MAXSTEP 200 PRINT FORCES ON RHOOUT ELECTROSTATIC POTENTIAL ELF PARAMETERS 0.0 0.0 STRUCTURE BONDS ANGLES DIHEDRALS &END &DFT FUNCTIONAL LDA GC-CUTOFF 5.0e-6 &END &SYSTEM SYMMETRY 8 POINT GROUP AUTO ANGSTROM CELL 3.797 1.69528575 4.86542 0.0 0.0 0.0 CUTOFF 120.0 CHARGE 0.0 &END &ATOMS *[Link] LMAX=P 4 3.014818112 2 680681888 2.680681888 0.782181888 1.116318112 *[Link] LMAX=D 4 1.249212986 0.649287014 2.547787014 3.147712986 *[Link] LMAX=D 4 2.897111043 2.798388957 0.899888957 0.998611043 *[Link] LMAX=P 20 0.261992993 2 540193112 2.540193112 1.769401965 3.428690989 1.059363053 1.636507007 3 155306888 3.155306888 0.129098035 2.266809011 0.839136947 3.535007007 1.256806888 2.027598035 0.368309011 2.737636947 2.160492993 0.641693112 3 667901965 3.667901965 1.530190989 2.957863053 &END 1.609250000 7.210402167

1.609250000 14.986109219 4 4.827750000 827750000 5 5.749109219 749109219 4.827750000 3.487890781 1.609250000 12.724890781

1.609250000 0.568999197 4.827750000 9.805999197 4.827750000 17.905000803 1.609250000 8.668000803

1.609250000 1 1.609250000 609250000 1.609250000 1.609250000 1.609250000 4.827750000 4 4.827750000 827750000 4.827750000 4.827750000 4.827750000 4.827750000 4.827750000 4.827750000 4.827750000 4.827750000 1.609250000 1.609250000 1 1.609250000 609250000 1.609250000 1.609250000

1.089966007 -0.147792007 0 147792007 2.032139989 3.491585919 17.051501595 10.326966007 9 9.089207993 089207993 11.269139989 12.728585919 7.814501595 17.384033993 18.621792007 16.441860011 14.982414081 19.896498405 8.147033993 9.384792007 7 7.204860011 204860011 5.745414081 10.659498405

1.609250000 2.026597833 4.827750000 11.263597833 4.827750000 16.447402167

Introduction to Computational Chemistry

CPMD Input file 2 (NMR Calculation)

&CPMD LINEAR RESPONSE RESTART ALL LATEST CONVERGENCE ORBITALS 1.0d-7 STRUCTURE BONDS ANGLES &END &RESP NMR FULL &END &DFT FUNCTIONAL LDA GC-CUTOFF 1.0e-6 &END &SYSTEM SYMMETRY 8 ANGSTROM CELL 3.797 1.69528575 4.86542 0.0 0.0 0.0 CUTOFF 120.0 CHARGE 0.0 &END &ATOMS ISOTOPES 39.00 48.00 181 00 181.00 16.00 *[Link] LMAX=P 4 3.014818112 2.680681888 0.782181888 1.116318112 *[Link] LMAX=D 4 1.249212986 0.649287014 2 547787014 2.547787014 3.147712986 *[Link] LMAX=D 4 2.897111043 2.798388957 0.899888957 0.998611043 *[Link] LMAX=P 20 0.261992993 2.540193112 1.769401965 3.428690989 1 059363053 1.059363053 1.636507007 3.155306888 0.129098035 2.266809011 0.839136947 3.535007007 1.256806888 2.027598035 0.368309011 2.737636947 2 160492993 2.160492993 0.641693112 3.667901965 1.530190989 2.957863053 &END 4.827750000 11.263597833 4.827750000 16.447402167 1.609250000 7.210402167

1.609250000 14.986109219 4.827750000 5.749109219 4.827750000 3.487890781 1.609250000 12.724890781

1.609250000 0.568999197 4.827750000 9.805999197 4 4.827750000 827750000 17 17.905000803 905000803 1.609250000 8.668000803

1.609250000 1.609250000 1.609250000 1.609250000 1 1.609250000 609250000 4.827750000 4.827750000 4.827750000 4.827750000 4.827750000 4.827750000 4.827750000 4.827750000 4.827750000 4.827750000 1 1.609250000 609250000 1.609250000 1.609250000 1.609250000 1.609250000

1.089966007 -0.147792007 2.032139989 3.491585919 17 17.051501595 051501595 10.326966007 9.089207993 11.269139989 12.728585919 7.814501595 17.384033993 18.621792007 16.441860011 14.982414081 19.896498405 8 8.147033993 147033993 9.384792007 7.204860011 5.745414081 10.659498405

1.609250000

2.026597833

Introduction to Computational Chemistry

ABINIT
ABINIT is a package whose main program allows one to find the total energy, charge density and electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density F Functional ti l Th Theory (DFT), (DFT) using i pseudopotentials d t ti l and d a planewave l basis.

Introduction to Computational Chemistry

ABINIT Input
To run abinis you need four things: (1) Access to the executable, abinis/abinip. (2) ( ) An input p file. (3) A files file (list of file names in a file). (4) A pseudopotential input file for each kind of element in the unit cell.

Introduction to Computational Chemistry

Sample file of filelist

tparal_1.filelist
tparal_1.in t tparal_1.out l 1 t tparal_1i tparal_1o tparal 1 tparal_1 [Link] The main input filename The main output filename The root of input files The root of f output files f The root of temporary files The pseudopotential file name
Introduction to Computational Chemistry

Sample input control file

tparal 1 in tparal_1.in
# # Lead crystal # # Simulation parameters ecut 30.0 acell 10.0 10.0 10.0 rprim 0.0 0.5 0.5 0.5 0.0 0.5 0.5 0.5 0.0 # K-points g p 888 ngkpt kptopt 1 nshiftk 4 shiftk 0.5 0.5 0.5 0.5 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.5 occopt 7 tsmear 0.01 # System y description ntypat 1 znucl 82 natom 1 typat 1 xred 0.000 0.000 0.000 nband 4 # SCF procedure nstep 3 tolvrs 1.0d-10 # This line added when defaults were changed (v5.3) to keep the previous old behaviour previous, iscf 5

Introduction to Computational Chemistry

Sample pseudopotential file

[Link]
Hartwigsen-Goedecker-Hutter psp for Pb, from PRB58, 3641 (1998) 82 4 010605 zatom,zion,pspdat t i d t 3 1 2 0 2001 0 pspcod,pspxc,lmax,lloc,mmax,r2well 0.617500 0.753143 0.000000 0.000000 0.000000 rloc, c1, c2, 0.705259 1.979927 -0.164960 -0.806060 rs, h11s, h22s, p h11p, p h22p, p 0.846641 0.864420 -0.540969 0.000000 rp, 0.207711 0.012948 0.000000 0.971939 0.374967 0.000000 0.000000 rd, h11d, h22d, 0.029256 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 rf, h11f, h22f, 0 000000 0.000000 0 0.000000 000000 0 0.000000 000000

c3, c4 h33s h33p p k11p, k22p, k33p h33d k11d, k22d, k33d h33f k11f k11f, k22f k22f, k33f

Introduction to Computational Chemistry

Sample PBS Job script

#PBS -l nodes=1:ppn=2 #PBS -l walltime=[Link] #PBS -j j oe #PBS -N test_abinitp # cd $PBS $PBS_O_WORKDIR O WORKDIR # mpirun /usr/global/abinit/5.4/bin/abinip < tparal_1.files > tparal_1.log exit

Introduction to Computational Chemistry

Molecular Mechanics Packages

AMBER CHARMM DL_POLY GROMACS LAMMPS NAMD XPLOR Towhee (MC)

Introduction to Computational Chemistry

AMBER (Assisted Model Building with Energy Refinement)

Classical molecular dynamics simulations (NVT, NPT, etc) Force field for biomolecular simulations (proteins, nucleic acids, carbohydrates and organic molecules) Combined Quantum Mechanics/Molecular Mechanics (QM/MM) implementation Parallelized dynamics y codes Explicit Solvent Models with particle-mesh Ewald sum (PME), Implicit Solvent models with Poisson-Boltzmann and Generalized Born approach pp Enhanced sampling (replica exchange MD, Locally Enhanced Sampling) Free energy calculation (MM/PBSA (MM/PBSA, etc etc.) ) Structural and trajectory analysis

Introduction to Computational Chemistry

Normal procedure to set up a simulation

Step 1, obtain and edit initial structure Step 2, prepare input parameter and topology file Step 3, run simulations and save production trajectory Step 4, analyze output and trajectory files
Preparatory Programs g Simulation Programs

PDB File

LEaP antechamber

Sander PMEMD NMode

Ptraj MM/PBSA

Analysis P Programs

Introduction to Computational Chemistry

Preparation using Leap

Leap command script
source leaprc.ff03 oxy = loadPdb [Link] b d [Link] bond 1 SG [Link] 6 SG charge oxy check oxy saveAmberParm oxy oxy_vac.top oxy_vac.crd solvateOct oxy TIP3PBOX 9.0 saveAmberParm oxy [Link] oxy top [Link] oxy crd quit

Introduction to Computational Chemistry

Sander Input

Introduction to Computational Chemistry

Analysis using ptraj

RMSD analysis (ptraj [Link] ptraj.input2)
trajin 1qs4A_md01_nowat.mdcrd reference [Link] rms reference out 1qs4A 1qs4A_md01_RMSD.dat md01 RMSD dat :1-154 go

B factor calculation B-factor

trajin 1qs4A_md01_nowat.mdcrd rms first out 1qs4A_md01_CA.dat :1154@CA atomicfluct t i fl t out t 1 1qs4A_md01.bfactor 4A d01 bf t @CA byatom bfactor go

Introduction to Computational Chemistry

Other Packages
3D-DOCK AUTODOCK Gaussview HADDOCK Molden M ld Pymol Rosetta VMD

Introduction to Computational Chemistry

Quantum mechanics/molecular mechanics method

Enhanced ONIOM Method (Gaussian)
o able to model large molecules by defining two or three layers within the structure that are treated at different levels of accuracy; o applicable in many other areas, including enzyme reactions cluster models of surfaces and surface reactions, reactions, photochemical processes, substituent effects and reactivity of organic and organometallic compounds, and homogeneous catalysis. Q-Chem/CHARMM, Gaussian/Tinker, ChemShell, NWChem, etc. o Interface Quantum mechanics with molecular mechanics directly with special treatment at the bourdary

Introduction to Computational Chemistry

Gaussian ONIOM Input

Two Layer ONIOM Two-Layer specification
# ONIOM(mp2/6-311g**:b3lyp/6-31g*:hf/3-21g) 3-layer ONIOM 0 C O H C C H H H H H 1 0 1 0 1 -0.006049274275 0.011403425950 0.944762558657 -1.307562483867 -1.047480751885 -1.903669606697 -1.903669606697 -1.988817319373 1 988817319373 -0.482972255230 -0.482972255230

# oniom(blyp/3-21g:amber) geom=connectivity ti it
# oniom(blyp/3-21g/dga1:amber) geom=connectivity opt=loose

0 1 0 1 0 blyp/3-21g:amber 1 0 1 with density fitting from Luecke 0.000000000000 0.066754956170 H 0.000000000000 1.308239478983 H 3 1 1 1 N-N3-0.181200 22.076181 24.563316 -13.077047 L 0.000000000000 -0.507359536461 H C-CT-0.003400 20.736756 0.000000000000 -0.766510748030 M H 1 24.514869 0.723886 -13.699982 0.723886 L0.723886 C-C-0.616300 20.734957 25.313129 -14.988472 L 0.000000000000 -2.301387120377 L H 4 24.680955 0.723886 -16.030293 0.723886 L0.723886 O-O--0.572200 20.731825 -0.885256630266 -0.468844831106 M 0.885256630266 -0.468844831106 M C-CT--0.043900 19.775830 32.473200 7.920456 L C 842389774687 CT 0 015800 18 18.776883 33.512258 512258 7 7.403331 403331 L H H-HC HC 0 0 0. 0 0. 0 0.000000000000 000000000000 -2.842389774687 2C-CT--0.015800 L776883 33 C-CT--0.082400 17.966350 32.942557 6.232525 H 0.881286097766 -2.591806824941 L C-CT-0.377886 16.928731 33.900731 5.689445 H -0.881286097766 -2.591806824941 L N-N2--0.693824 17.521649 35.160530 5.191031 H
N-N--0.415700 22.301376 31.316157 8.955475 L H-HW-0.417000 H HW 0.417000 10.154733 46.125705 25.662719 L H-HW-0.417000 11.339041 47.039598 25.433539 L H-H-0.274700 21.866560 34.137178 7.953109 L H-H-0.377886 17.847763 35.188083 4.238902 H H-H-0.341200 18.066775 49.503351 -1.731201 L H-HO-0.474700 15.931300 31.668829 17.328019 L 1772 1.0

Three-Layer ONIOM specification

( p g yp g 1 2 1.0 g) # ONIOM(mp2/6-311g**:b3lyp/6-31g*:hf/3-21g) 1770 1.0

Introduction to

1771 1.0 2 3 1.0 5 1.0 1769 1.0 3 4 2.0 8 2.0 4 5 6 1.0 7 Chemistry 1.0 1764 1.0 Computational 6 1768 1.0

Visualization tools
Molecules Gaussview Molden M ld Molekel Pymol ECCE ArgusLab VMD VegaZZ DeepView Discovery Studio JMol Periodic Systems
Materials Studio Crystal y Maker VMD

Introduction to Computational Chemistry

MOLDEN

Introduction to Computational Chemistry

Gaussview

Introduction to Computational Chemistry

VMD

Introduction to Computational Chemistry

ArgusLab

Introduction to Computational Chemistry

Acknowledgement

Some slides have used pictures and graphics from other authors.

Introduction to Computational Chemistry