intro compchem

7/29/2019 Intro CompChem

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Materials Simulation Center presents:

Introduction toComputational Chemistry



Course contents

• verv ew: a s ompu a ona em s ry

• 1: ab initio method

• 2: Density Functional Theory

• 3: Molecular mechanics method

Introduction to Computational Chemistry



Overview: What is Computational Chemistry

Computational Chemistry uses the results of theoreticalchemistry, incorporated into efficient computer programs, tocalculate 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. semi-empirical method), to very approximate (i.e. Molecular

, - .

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, relativeenergies, charge distributions, dipoles and multipole moments,

,quantities, etc.




Simulation method for length and time scale

ContinuumContinuumContinuumContinuum

-3

100

TIME

/s

Mesoscale methodsAtomistic

e o s

-3

100

TIME

/s


e o s

-3

100

TIME

/s


e o s

-3

100

TIME

/s


e o s

-9

10-6(μs)

mu a onMethods

Semi-empirical

Lattice Monte Carlo

Brownian dynamicsDissipative particle dyn

-9

10-6(μs)

mu a onMethods

Semi-empirical

Lattice Monte Carlo


-9

10-6(μs)

mu a onMethods

Semi-empirical

Lattice Monte Carlo


-9

10-6(μs)

mu a onMethods

Semi-empirical

Lattice Monte Carlo


-15

10-12(ps)

me o s

Ab initio

methods

Monte Carlo

molecular dynamics

tight-bindingMNDO, INDO/S-15

10-12(ps)

me o s

Ab initio

methods

Monte Carlo

molecular dynamics


10-12(ps)

me o s

Ab initio

methods

Monte Carlo

molecular dynamics


10-12(ps)

me o s

Ab initio

methods

Monte Carlo

molecular dynamics

tight-bindingMNDO, INDO/S

10-10 10-9 10-8 10-7 10-6 10-5 10-4

(nm) (μm)

LENGTH

10-10 10-9 10-8 10-7 10-6 10-5 10-4

(nm) (μm)

LENGTH

10-10 10-9 10-8 10-7 10-6 10-5 10-4

(nm) (μm)

LENGTH

10-10 10-9 10-8 10-7 10-6 10-5 10-4

(nm) (μm)

LENGTH

/meters /meters

Figure 1. Schematic illustration of the simulation

/meters /meters

Figure 1. Schematic illustration of the simulation




Methods

• n t o quantum c em stry met o s

• 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




Ab initio quantum chemistry methods

Ab initio quantum chemistry solves electronic Schrödinger equation frommathematical principles. The term ab initio indicates that thecalculation is derived from first principles and does not rely on anyemp r ca a a.




Commonly used methods

Hartree-Fock methods

o Hartree-Fock (HF)o Restricted Open-shell Hartree-Fock (ROHF)o Unrestricted Hartree-Fock (UHF)

Post-Hartree-Fock methods

-o Configuration interaction (CI)o Coupled cluster (CC)

o Quadratic configuration interaction (QCI)o uan um c em s ry compos e me o s , ,

Multi-reference methods

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




Electron atomic and molecular orbitals

HOMO LUMO

HOMO-1 LUMO+1

HOMO-2

LUMO+2

-

+


HOMO-4 LUMO+4



Molecular Orbital Theory & Hartree-Fock Method

)2()2()2(

)1()1()1(

1

N21

φφφ

φφφ

L

L

N

) N() N() N(! N

N21 φφφ

=ψ

L

LLLL

χ==μ

μμii c

1

LCAO: Linear Combination of Atomic Orbitals

N

Hartree-Fock (HF)

=μμμii

1

Variation Principle




Post-Hartree-Fock Method




Basis Set

STO

∑ χ=φ=

μμ N

ii c

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*)

• use unc ons are eno e y + - +

* The selection of basis set is a key factor to the accuracy of the numeric solution.




Level of Theory




Cost vs. Accuracy




Methods













Density functional theory methods

• -

― All properties of the many-body system are determined by the

― Each property is a functional of the ground state density n0(r) which

―

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

pro em – a can e so ve• The ground state density is required to be the same as the exact

density




Exchange-Correlation Functional

• Local Density Approximation - LDA

Exc can be determined usin homo eneous electron as model or using quantum Monte Carlo methods

• -




Correlation-Exchange Functional

LDAlocal density

l c o s t

VWN5

BLYP

GGAgradient corrected

p u t a t i o n

BP86

Meta-GGAkinetic energy density

included t y a n d c oTPSS

M06-L

Hybrid“exact” HF exchange

s i n g q u a l i

B3LYPB97/2MPW1K

Hybrid-meta-GGA I n c r e a

MPWB1KM06




Software supporting DFT


http://en.wikipedia.org/wiki/Density_functional_theory



Methods













Semi-empirical quantum chemistry method

CNDO (1965,CNDO (1965, PoplePople et al)et al)

MINDO (1975, Dewar )MINDO (1975, Dewar )

STOSTO--basis (/Sbasis (/S--spectra,/2 dspectra,/2 d--orbitalsorbitals))

//1/2/3, organics1/2/3, organics

MNDO (1977,MNDO (1977, ThielThiel)) /d, organics, transition metals/d, organics, transition metals

INDO (1967,INDO (1967, PoplePople et al)et al)

ZINDOZINDO

rgan csrgan cs

Electronic spectra, transition metalsElectronic spectra, transition metals

SINDO1SINDO1 11--3 row binding energies,3 row binding energies,

photochemistry and transition metalsphotochemistry and transition metals




Further improvement

AM1 AM1 Modified nuclear repulsion terms model to account for Modified nuclear repulsion terms model to account for

-- ,,

Widely used today (transition metals,Widely used today (transition metals, inorganicsinorganics))

PM3 (1989, Stewart)PM3 (1989, Stewart)

Larger data set for parameterization compared to AM1Larger data set for parameterization compared to AM1 Widely used today (transition metals,Widely used today (transition metals, inorganicsinorganics))




Methods













Molecular mechanics method

Interactions between atoms (Potential Energy Function) are representedby functions of distance, angle or dihedral

Collection of empirical parameters and potential functions is known as aforce field.

i.e. AMBER

force field:




Commonly used force field

AmberDNA, proteins and lipids. Generalized Amber Force Field (GAFF) covers most organicspace.

OPLSOrganic molecules in the liquid phase. Available as all-atom (AA) or united-atom (UA)form.

CHARMM DNA, proteins, lipids, sugars.

GROMOS General purpose. Organic and biochemical space.

Dreiding General purpose. Includes some parameters for metals and main group elements.

MM2/MM3General purpose. MM2 used for hydrocarbons. MM3 includes most of organic space plussome other main rou and metal atom t es.

Water Rigid and flexible models available. TIP3P widely used in biological simulation.




Commonly used softwares




Common tasks

• Sampling conformational spaces (Structure and dynamics)

•

• Structural refinement (based on NMR data)

• Reaction path (Transition Path Sampling)

• Molecular interaction (Ligand-Protein)

• Investigate mutational effects

• etc.




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

•

• Simulation of finite temperature behaviour and phase changes




Methods






― Periodic Electronic Structure Calculations

― Ewald summation for long-range interaction






Systems with periodic boundary condition

• , ,(polymers) and 0D (molecule))




Bloch’s Theorem

e e ec ron c wave unc on n a per o c po en a can eexpressed as

.ex r r ik cr =

r unk

k is wavevector within the first Brillouin zone

nk n




Plane wave and pseudopotential

ane wave as s se s a na ura c o ce or e per o celectronic wave function due to its periodicity and itsmathematical and computational convenience.

).(exp)( r ik cr ik k i Σ=Ψ

Application of pseudopotentialcan effectively:

• reduce the size of basis set ;• reduce the size of the system

(less electrons)

• take into account of the




Long-range interaction in Molecular Mechanics

Ewald O(N 3/2 ) Ewald, 1921

summation

Fast MultipoleMethod

O(N) Greengard, 1987

Particle Mesh O N lo N Darden, 1993

EwaldMulti-gridsummation

O(N) Brandt et al., 1990

Skeel et al., 2002

Izaguirre et al., 2003




Computational Chemistry Codes on Clusters

• ― GAMESS― GAUSSIAN―

― NWCHEM― ORCA―

― SPARTAN― TURBOMOLE

• Quantum chemistry package for solids/surface― ― ―

• Molecular Mechanics Packa es

― CPMD

― NWCHEM

― AMBER― CHARMM― DL_POLY

― GROMACS― LAMMPS― NAMD

― XPLOR

• Others― 3D-DOCK― AUTODOCK

― Molden― Pymol

― VMD


― HADDOCK ― Rosetta



Molecular Quantum Chemistry Packages




Quantum Chemistry package on clusters

― GAMESS (US) ― QCHEM

―

―NWCHEM

―

―TURBOMOLE

― ORCA




GAMESS

• General Atomic and Molecular Electronic Structure System

― Primary focus is on ab initio quantum chemistry calculations

― Also includes DFT semi-em irical AM1 PM3 and QM/MMcapabilities

• Early version of GAMESS is available under /usr/global/gamess

― scripts need to execute the program




GAMESS Input file

$CONTRL SCFTYP=RHF RUNTYP=OPTI MI ZE COORD=CART

NZVAR=0 MULT=1 I CHARG=0 $END

SYSTEM TI MLI M=20000 MEMORY=10000000 END

$STATPT NSTEP=1000 $END

$BASI S GBASI S=STO NGAUSS=3 $END

$GUESS GUESS=HUCKEL $END

$DATA

Test . . . HCHO mol ecul e - RHF/ STO- 3G ( a comment l i ne)

Cn 1

C 6. 0 0. 6084782705 - 0. 0000011694 0. 000000000000

O 8. 0 - 0. 6082418894 - 0. 0000002093 0. 000000000000

H 1. 0 1. 2040919862 - 0. 9264398115 0. 000000000000

H 1. 0 1. 2040973125 0. 9264340484 0. 00000000000$END


GAUSSIAN



GAUSSIAN

Gaussian 03 is a general electronic structure programs. Gaussian 03 isused by chemists, chemical engineers, biochemists, physicists andothers for research in established and emerging areas of chemicaln eres .


G i I t Fil St t



Gaussian Input File Structures

Route section (# lines): Specify calculation type, model chemistry and other optionsTitle section: Brief description of the calculationMolecule specification: Specify molecular system to be studied

%NPr ocShar ed=2 Link 0 section (#of processors for SMP)

Optional additional sections: Additional input needed for specific job types

=%chk=h2o_opt . chk# RHF/ 6- 31g** OPT

(checkpoint file name and location)

Route section

- g op m za on

0 1O

Molecule Specification section (charge, multiplicity)Structure representation in Z-matrix format

r

H 1 r1 2 t ha1

r 1 1. 000


a .

R t S ti K d



Route Section: Keywords

ADMP ExtendedHuckel MaxDisk Scan

AM1 External MINDO3 SCF

Amber ExtraBasis MM SCRF

Archive Frozen Core Options MNDO SP

B3LYP Field MP* Keywords Sparse

BD FMM Name Stable

BOMD Force NMR Symmetry

CASSCF Frequency ONIOM TD

*

CBSExtrapolate Gen Output Test

CCD Geom OVGF TestMO

Charge GFInput PBC TrackIO

ChkBasis GFPrint PM3 Transformationuess o ar

CIS GVB Population Units

CNDO Hartree-Fock Pressure Volume

Complex Huckel Prop W1U

Constants INDO Pseudo Zindo

Counterpoise Integral Punch Link 0 Commands

CPHF IOp QCISD Non-Standard Routes

Density IRC ReArchive Program Development Keywords

DensityFit IRCMax SAC-CIDensity Functional Methods


K d (J b t )



Keywords (Job types)

• ng e po nt energy.•Opt Geometry optimization.

•Freq Frequency and thermochemical analysis.

•IRC Reaction path following.

•IRCMax Find the maximum energy along a specific reaction path.

•Scan Potential energy surface scan.

•Polar Polarizabilities and hyperpolarizabilities.

•ADMP and BOMD Direct dynamics trajectory calculation.

• .

•Volume Compute molecular volume.


Keywords (Molecular properties)



Keywords (Molecular properties)

, ,o Electron affinities and Ionization potentials via propagator methods: OVGF

o Electron density: cubegen

o Electronic circular dichroism: TD

,o Electrostatic-potential derived charges: Pop=Chelp, ChelpG or MK

o Frequency-dependent polarizabilities/hyperpolarizabilities: Polar CPHF=RdFreqo High accuracy energies: CBS-QB3, G2, G3, W1U

o Hyperfine spectra tensors (incl. g tensors): Freq=(VCD, VibRot[, Anharmonic])

o Hyperpolarizabilities: Freq, Polar

o IR and Raman spectra: Freq

= o NMR shielding and chemical shifts: NMR

o NMR spin-spin coupling constants: NMR=SpinSpin

o Optical rotations: Polar =OptRot CPHF=RdFreq

,

o Thermochemical analysis: Freqo UV/Visible spectra: CIS, Zindo, TD

o Vibration-rotation coupling: Freq=VibRot

=


Available model calculations



Available model calculations


Keyword (Basis set)



Keyword (Basis set)Basis Set Applies to Polarization Functions Diffuse Functions

STO-3G H-Xe *3-21G H-Xe * or ** +

6-21G H-Cl (d)

4-31G H-Ne (d) or (d,p)

6-31G , 6-311G H-Kr (3df,3pd) ++

D95 H-Cl except Na and Mg (3df,3pd) ++

D95V H-Ne (d) or (d,p) ++

SHC H-Cl *

CEP-4G , CEP-31G, CEP121G H-Rn * (Li-Ar only)

- -,

LanL2DZ H, Li-Ba, La-Bi

SDD, SDDAll all but Fr and Ra

cc-pV(DTQ5)Z H-He, B-Ne, Al-Ar, Ga-Kr included in definition added via AUG- prefix

- , - -

SV , SVP H-Kr in SVP

TZV and TZVP H-Kr included in definition

MidiX H, C-F, S-Cl, I, Br included in definition

- -- , - , , , , ,

UGBS H-Lr UGBS(1,2,3)PMTSmall H-Ar

DGDZVP H-Xe

DGDZVP2 H-F, Al-Ar, Sc-Zn


DGTZVP H, C-F, Al-Ar

Molecular Specification



Molecular SpecificationMolecules can be s ecified b Z- matrix or Cartesian coordinate.

The Z-matrix is a way to represent asystem u t o atoms. t prov es a

description of each atom in a moleculein terms of its atomic number, bond, ,

angle, the so-called internal

coordinates.

Some softwares provide sketcher and fragment library to build molecules with’

Molecular builders

, . . , , ,

Molecular Editor, HyperChem, Gabedit, etc.

Some softwares provide interface to write out z-matrix or Cartesian


coordinates, i.e. Molden

NWCHEM



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

―


NWCHEM Input file format



NWCHEM Input file format

s ar wa er

Ti t l e “H2o ener gy”

•Job name determines namesfor temporary files

•

geomet r y uni t s auO 0. 00000 0. 000000 0. 000000

-

change settings for futurecalculations

H 0. 00000 - 1. 43042809 - 1. 10715266

End

•task directive triggers

calculation

• - -Basi s

* l i br ar y 3- 21G

End

bottom (only settings above a

task have an impact)

MP2; f r eeze at omi c; END

Task mp2 ener gy

•Python procedures for morecomplicated structures


Quantum chemistry package for solids/surface



Quantum chemistry package for solids/surface

― ABINIT ― CASTEP

― ADF/Band

― CPMD

― NWCHEM

― VASP


VASP (Vienna Ab-initio Simulation Package)



VASP (Vienna Ab initio Simulation Package)

VASP is a complex package for performing ab-initio quantum-mechanicalmolecular dynamics (MD) simulations using pseudopotentials or theprojector-augmented wave method and a plane wave basis set.

• The approach implemented in VASP is based on the (finite-temperature) local-density approximation with the free energy asvariational quantity and an exact evaluation of the instantaneouselectronic ground state at each MD time step. VASP uses efficient

matrix diagonalisation schemes and an efficient Pulay/Broyden chargeens y m x ng.

• The interaction between ions and electrons is described by ultra-softVanderbilt pseudopotentials (US-PP) or by the projector-augmentedwave me o .

• Forces and the full stress tensor can be calculated with VASP andused to relax atoms into their instantaneous ground-state.


VASP Input



VASP Input

INPUT Files

POSCAR

OUPUT Files

OUTCAR

KPOINTS CONTCAR

WAVECAR

EIGENVALPROCAR

XDATCARSTOPCAR is used to

LOCPOTDOSCAR

signal stopping VASPexecution


Structure Input File



Structure Input File


Pseudopotential File



Pseudopotential File


KPOINT Sampling



p g


CONTROL File




Result analysis



y


CPMD



e co e s a p ane wave pseu opotent a mp ementat on oDensity Functional Theory, particularly designed for ab-initiomolecular 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 constantpressure

― path integral MD

― response functions

― exc e s a es

―many electronic properties

― time-dependent DFT (excitations, molecular dynamics in excited states)


CPMD Input file 1 (Wave Function)



&CPMD 120.0 0.998611043 1.609250000 7.210402167

OPTIMIZE WAVEFUNCTIONCONVERGENCE ORBITALS

1.0e-8

MAXSTEP

200

CHARGE0.0

&END

&ATOMS

*O-q6.psp

LMAX=P

20

0.261992993 1.609250000 1.089966007

RHOOUT

ELECTROSTATIC POTENTIAL

ELF PARAMETERS

0.0 0.0

*K-q9.psp

LMAX=P

4

3.014818112 1.609250000 14.986109219

. . - .

1.769401965 1.609250000 2.032139989

3.428690989 1.609250000 3.491585919

1.059363053 1.609250000 17.051501595

1.636507007 4.827750000 10.326966007

&END

&DFT

FUNCTIONAL LDA

GC-CUTOFF

. . .

0.782181888 4.827750000 3.487890781

1.116318112 1.609250000 12.724890781

*Ti-q12.psp

LMAX=D

. . .

0.129098035 4.827750000 11.269139989

2.266809011 4.827750000 12.728585919

0.839136947 4.827750000 7.814501595

3.535007007 4.827750000 17.384033993

1.256806888 4.827750000 18.6217920075.0e-6

&END

&SYSTEM

SYMMETRY

4

1.249212986 1.609250000 0.568999197

0.649287014 4.827750000 9.805999197

2.547787014 4.827750000 17.905000803

3.147712986 1.609250000 8.668000803

2.027598035 4.827750000 16.441860011

0.368309011 4.827750000 14.982414081

2.737636947 4.827750000 19.896498405

2.160492993 1.609250000 8.147033993

0.641693112 1.609250000 9.384792007

POINT GROUP

AUTO

ANGSTROM

CELL

*Ta-q13.psp

LMAX=D

4

2.897111043 1.609250000 2.026597833

. . .

1.530190989 1.609250000 5.745414081

2.957863053 1.609250000 10.659498405

&END

. . . . . .

CUTOFF

. . .

0.899888957 4.827750000 16.447402167


CPMD Input file 2 (NMR Calculation)



&CPMD &END 2.798388957 4.827750000 11.263597833

LINEAR RESPONSERESTART ALL LATEST

CONVERGENCE ORBITALS

1.0d-7

STRUCTURE BONDS ANGLES

&ATOMS

ISOTOPES

39.00

48.00

0.899888957 4.827750000 16.4474021670.998611043 1.609250000 7.210402167

*O-q6.psp

LMAX=P

&RESP

NMR

FULL

.

16.00

*K-q9.psp

LMAX=P

0.261992993 1.609250000 1.089966007

2.540193112 1.609250000 -0.147792007

1.769401965 1.609250000 2.032139989

3.428690989 1.609250000 3.491585919

&DFT

FUNCTIONAL LDA

GC-CUTOFF

1.0e-6

3.014818112 1.609250000 14.986109219

2.680681888 4.827750000 5.749109219

0.782181888 4.827750000 3.487890781

1.116318112 1.609250000 12.724890781

. . .

1.636507007 4.827750000 10.326966007

3.155306888 4.827750000 9.089207993

0.129098035 4.827750000 11.269139989

2.266809011 4.827750000 12.728585919

0.839136947 4.827750000 7.814501595&END

&SYSTEM

SYMMETRY

8

*Ti-q12.psp

LMAX=D

4

1.249212986 1.609250000 0.568999197

0.649287014 4.827750000 9.805999197

3.535007007 4.827750000 17.384033993

1.256806888 4.827750000 18.621792007

2.027598035 4.827750000 16.441860011

0.368309011 4.827750000 14.982414081

2.737636947 4.827750000 19.896498405

CELL

3.797 1.69528575 4.86542 0.0 0.0 0.0

CUTOFF

120.0

. . .

3.147712986 1.609250000 8.668000803

*Ta-q13.psp

LMAX=D

. . .

0.641693112 1.609250000 9.384792007

3.667901965 1.609250000 7.204860011

1.530190989 1.609250000 5.745414081

2.957863053 1.609250000 10.659498405

0.0 2.897111043 1.609250000 2.026597833


ABINIT



ABINIT is a package whose main program allows one to find the totalenergy, charge density and electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density

unc ona eory , us ng pseu opo en a s an a p anewave

basis.


ABINIT Input



To run abinis you need four things:(1) Access to the executable, abinis/abinip.

2 An in ut 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.


Sample file of filelist



t par al _1. i n

tparal_1.filelist

par a _ . out par al _1it par al _1o

_ 82pb. 4. hgh

- The main output filename

- The root of input files

- The root of output files

- The root of temporary files

- The pseudopotential file name


Sample input control file



#

# Lead crystal

kptopt 1

nshiftk 4

typat 1

xred

_ .

#

# Simulation parameters

shiftk

0.5 0.5 0.50.5 0.0 0.0

0.000 0.000 0.000

nband 4

ecut 30.0

acell 10.0 10.0 10.0

rprim

0.0 0.5 0.0

0.0 0.0 0.5

occopt 7

# SCF procedure

nstep 3

tolvrs 1.0d-100.0 0.5 0.5

0.5 0.0 0.5

0.5 0.5 0.0

tsmear 0.01

# System description

# This line added whendefaults were changed(v5.3) to keep the

# K-points

ngkpt 8 8 8

ntypat 1znucl 82

natom 1

,

iscf 5


Sample pseudopotential file



Har t wi gsen- Goedecker - Hut t er psp f or Pb, f r om PRB58, 3641 ( 1998)

82pb.4.hgh

za om, z on, psp a

3 1 2 0 2001 0 pspcod, pspxc, l max, l l oc, mmax, r 2wel l

0. 617500 0. 753143 0. 000000 0. 000000 0. 000000 r l oc, c1, c2, c3, c40. 705259 1. 979927 - 0. 164960 - 0. 806060 r s, h11s, h22s, h33s

0. 846641 0. 864420 - 0. 540969 0. 000000 r p, h11p, h22p, h33p

0. 207711 0. 012948 0. 000000 k11p, k22p, k33p

0. 971939 0. 374967 0. 000000 0. 000000 r d, h11d, h22d, h33d

0. 029256 0. 000000 0. 000000 k11d, k22d, k33d

0. 000000 0. 000000 0. 000000 0. 000000 r f , h11f , h22f , h33f

. . . , ,


Sample PBS Job script



#PBS -l nodes=1:ppn=2#PBS -l walltime=4:00:00

#PBS - oe

#PBS -N test_abinitp

#

_ _

#

mpirun /usr/global/abinit/5.4/bin/abinip < tparal_1.files > tparal_1.log

exit


Molecular Mechanics Packages



― AMBER―

― GROMACS―

― XPLOR―

― DL_POLY ― NAMD


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 d namics codes

• Explicit Solvent Models with particle-mesh Ewald sum (PME), ImplicitSolvent models with Poisson-Boltzmann and Generalized Born

a roach• Enhanced sampling (replica exchange MD, Locally Enhanced

Sampling)

• , .

• Structural and trajectory analysis• ……


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

Pro rams

Simulation

Programs AnalysisLEaP

antechamber

Sander

PMEMD

rograms

PtrajMM/PBSA


Preparation using Leap



Leap command script

source leaprc.ff03

oxy = loadPdb oxyt.pdb

on oxy. . oxy. .

charge oxy

check oxysaveAmberParm oxy oxy_vac.top oxy_vac.crd

solvateOct oxy TIP3PBOX 9.0

. .

quit


Sander Input




Analysis using ptraj



RMSD analysis (ptraj 1qs4A.top ptraj.input2)t r aj i n 1qs4A_md01_nowat . mdcr d

r ef er ence 1qs4A. cr d_ _ .

: 1- 154go

-t r aj i n 1qs4A_md01_nowat . mdcr d

r ms f i r st out 1qs4A_md01_CA. dat : 1-154@CA

a om c uc ou qs _m . ac orbyat om bf act or

go


Other Packages



― 3D-DOCK ― Pymol

― AUTODOCK

―

― Rosetta

―

― HADDOCK

―o en


Quantum mechanics/molecular mechanics method



•

o able to model large molecules by defining two or three layers within the structure that are treated atdifferent levels of accuracy;

o applicable in many other areas, including enzyme,

reactions, photochemical processes, substituenteffects and reactivity of organic and organometalliccompounds, and homogeneous catalysis.

• Q-Chem/CHARMM, Gaussian/Tinker, ChemShell, NWChem, etc.

special treatment at the bourdary


Gaussian – ONIOM Input-



# ONIOM(mp2/6-311g**:b3lyp/6-31g*:hf/3-21g)

specification

# oniom(blyp/3-21g:amber)

3-layer ONIOM

0 1 0 1 0 1 0 1 0 1 0 1 0 1C -0.006049274275 0.000000000000 0.066754956170 H

O 0.011403425950 0.000000000000 1.308239478983 H

geom=connect v ty# oniom(blyp/3-21g/dga1:amber) geom=connectivity opt=loose

blyp/3-21g:amber with density fitting from Luecke

3 1 1 1

H 0.944762558657 0.000000000000 -0.507359536461 H

C -1.307562483867 0.000000000000 -0.766510748030 M H 1 0.723886 0.723886 0.723886

C -1.047480751885 0.000000000000 -2.301387120377 L H 4 0.723886 0.723886 0.723886

H -1.903669606697 -0.885256630266 -0.468844831106 M

H -1.903669606697 0.885256630266 -0.468844831106 M

N-N3-0.181200 22.076181 24.563316 -13.077047 L

C-CT-0.003400 20.736756 24.514869 -13.699982 L

C-C-0.616300 20.734957 25.313129 -14.988472 L

O-O--0.572200 20.731825 24.680955 -16.030293 L

……

C-CT--0.043900 19.775830 32.473200 7.920456 L

H -1.988817319373 0.000000000000 -2.842389774687 L

H -0.482972255230 0.881286097766 -2.591806824941 L

H -0.482972255230 -0.881286097766 -2.591806824941 L

- -- . . . . - . .

C-CT--0.082400 17.966350 32.942557 6.232525 H

C-CT-0.377886 16.928731 33.900731 5.689445 H

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 10.154733 46.125705 25.662719 L

Three-Layer ONIOM specification

# ONIOM m 2/6-311 **:b3l /6-31 *:hf/3-21

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


1 2 1.0 1770 1.0 1771 1.0 1772 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 1.0 1764 1.0

6 1768 1.0

Visualization tools



Molecules• Gaussview

Periodic Systems• Materials Studio• Cr stal Maker

• o en

• Molekel•

• VMD

• ECCE

• ArgusLab

• VMD

• VegaZZ

• Discovery Studio• JMol


MOLDEN




Gaussview




VMD




ArgusLab




Acknowledgement



graphics from other authors.


intro compchem

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