NTChem
NTChem()(.inpcsh)(bash(RCCS))

ntprepntprep/opt/aics/ntchem/scripts(RCCS)
ccpg: /local/apl/pg/ntchem/scripts

ccuv: /local/apl/uv/ntchem/scripts

Focus: /home1/share/NTChem/ntchem2013.4.0/scripts
ntprep(1)xmol xyz(2) .bash_profile

ntprep.bash_profile

$PATH

*
# User specific environment and startup programs$ PATH=$PATH: /opt/aics/ntchem/scripts$ export PATH
(3)
ntprep

NTChemntprepntprep.basis(4)

ntprepcdntprep$ cd ~/my_ntchem_wrkdirEnterntprepntprep

$ ntprep(5)“Enter geometry file name:”
xmol xyz

Enter:

h2o.xyzh2o.xyz [Enter](6) NTChem“Enter input file name”

NTChemEnter: NTChemh2o_dft_opt.inp

h2o_dft_opt [Enter]
Enter

(3)

(3)

h2o.xyzh2o.inp(7)“Select the type of task”
1EnterEnter:
3 [Enter](8)“Select the quantum chemistry method”
DFTEnterEnter:

HF

1 [Enter](9)“Select how to assign the basis set”
Enter
2

Enter, “Select the basis set for”

Def2-SVP

Enter
Enter, ”0”Enter”Select basis set card”
Enter:”mybasis.basis”

mybasis.basis [Enter](10)“Select the scalar relativistic Hamiltonian”
EnterEnter:

DK

2 [Enter]“Select the spin-orbit relativistic Hamiltonian”
EnterEnter
:

-

DK3-

DK12[Enter]
2[Enter](11)“Define the total charge”
(0)

Enter
Enter:-1 [Enter]

-1

(12)
“Define the spin multiplicity”
(12)

Enter
Enter:

33 [Enter](13) SCF“Select the type of SCF”
SCF

SCF

(

1Restricted

1Unrestricted)

Enter

SCF

SCF
:

3EnterSCF

Restricted-Open

2 [Enter](14) DFT(7)

DFT“Select the DFT exchange-correlation functional”

DFTwB97XDEnterEnter: DFT

B3LYP

3 [Enter](15) SCF

Fock

2Coulomb“Select the method for evaluation of Coulomb contribution in SCF”
Fock2SCFCoulomb

2Enter2RIEnter(16) SCF“Select the SCF initial guess”
NDDO

Enter
Enter:
3 [Enter]

NTChem.MO(17) TD-DFT (TD-HF)
HF

((6)

DFT

1(7))

“Calculate the excitation energy by TD-DFT(TD-HF)”

TD-DFT (TD-HF)

Enter
2Enter”Select the TD approximation”

TD-DFT (TD-HF)
RPAEnter

TDA

2Enter” Define the numberof excited states”
EnterEnter
RHF

SCF” Select target state”,1Enter32Enter(18) Mulliken“Calculate the Mulliken populations”

Mulliken

MullikenEnterMulliken

2Enter
(19)“Calculate the electrostatic potential”
Enter2Enter(20)“Perform the parallel calculations”
Enter2Enter”Define number of nodes used for parallelcalculations”:
128 [Enter]
(21)

Enter
128

“Define the job time limit in hh:mm:ss”
1Enterhh:mm:ss:
18:30:00 [Enter]

1830

Enter

NTChem

NTChemntprepinp.bashpjsub: ntprep

NTChemh2o_dft_opt.bash$ pjsub h2o_dft_opt.bash
NTChem

NTChemntprepinp.csh: ntprep

jsub

NTChemh2o_dft_opt.csh

ccpg$ jsub –q PF h2o_dft_opt.csh
NTChem.out(ab initio Molecular Dynamics)
gradient	 
RATTLE

Nosé–Hoover

Tully()

Geom

Velo

Velo
Velo
Vx1

Vy1

Vz1

VyN

VzN

...
VxN
End
Vx

Vy

Vzx

VelUnit = 'AngFs'

yz

&AIMD

Angstrom/Femto second

NormMod
Geom
Classical
Quantum&AIMD

VibSample

Classical
Quantum

()

0()
&AIMD

RotSample = .TRUE.

1

1/2kT (k:T:(&AIMDKelvin))

2
2

2

Molecule1

Molecule2

Geom

Molecule1

Molecule2…

Geom!--- Molecule 1
Symbol1

X1

Y1

Z1

XN

YN

ZN

...
SymbolN!--- Molecule 2
Symbol(N+1)

X(N+1)

Y(N+1)

Z(N+1)...
Symbol(N+M) X(N+M) Y(N+M) Z(N+M)
End
Symbol X Y Z&AIMD

x y z
NAtom1=N

Molecule1

Molecule2

NAtom2=M

2&AIMD
Molecule1

CollSample = .TRUE.

Molecule2&AIMD

Distance

2&AIMD

ImpParam

2kT
T

&AIMD

Molecule1

KelvinMolecule2&AIMD

Molecule1

Z
OriSample = .TRUE.

Molecule2&AIMD

VibSample

NormMod

Geom
Molecule1

Prefix Name

RotSample&AIMDName1 = 'Name1'

Molecul2

Name2 = 'Name2'

NormMod

&AIMDMD

Kelvin

AIMD

AIMD

AIMD
&AIMD

Restart = .TRUE.

Nosé–Hoover chain&AIMD&AIMD

RATTLE

KelvinMD(H–X)

RATTLE&AIMD

RATTLE = .TRUE.

RATTLERATTLE
Num1

Num2...
NumN

NumM

End
Num

(Geom)

(NYI)
Tully
&AIMD
StateNum

SurfHopt = .TRUE.

Gradient

Ensemble(Molecular Mechanics)
Tinker&Tinker2NT

Param

TinXYZTinXYZ

TinkerXYZ

TinXYZ
1

SymbolX1

Y1

Z1

Param1

SymbolXN

YN

ZN

ParamNX

Y

Bond1-1

Bond1-2

Bond1-3...
N

BondN-1

BondN-2

BondN-3End
Symbol

Zx

Bondz
Geom

TinXYZKeyy

Prefix Name

ParamMMQM/MM
Quantum Mechanics (QM)

Molecular Mechanics (MM)QM

MMvan der Waals
QM

1Molecular Mechanics (MM)

MM

QM/MM

3

Name.inp
Name.QM.inp

QM

Name.MM.inp

MM

QM/MM

Geom&QMMM

NameQM NameMM

QM

MMQM

MM

Prefix Namevan der Waals&QMMM
TinXYZTinXYZ

Paramvan der Waals

TinkerXYZ

TinXYZ
1

Symbol1

X1

Y1

Z1

SymbolN

XN

YN

ZN

Param1

Bond1-1

Bond1-2

Bond1-3...
NN+1

Symbol(N+1)

Bond(N+1)-2

X(N+1)

ParamN

BondN-1

BondN-2

BondN-3

Y(N+1)

Z(N+1)

Param(N+1)

Bond(N+1)-1

Y(N+M)

Z(N+M)

Param(N+M)

Bond(N+M)-1

Bond(N+1)-3

...
N+M

Symbol(N+M)

Bond(N+M)-2

X(N+M)

Bond(N+M)-3

End
SymbolX

Y

Zx

Bondyz

Param

Geom

TinXYZ
QM
QM

Geom

Geom_ONIOMT

MM

QM

MM

Ch&MDInt1

CalChg = .TRUE.

QM
Geom_ONIOM!--- QM
Symbol1

X1

Y1

Z1

T

XN

YN

ZN

...
SymbolN

T!--- MMCh

X(N+1)

Y(N+1)

Z(N+1)

X(N+M)

Y(N+M)

Z(N+M)

Charge(N+1)...
Ch

Charge(N+M)

End
X Y Z

CX CY CZ

Charge

MM
MM

Geom
T

MM

TinXYZMM
Geom_ONIOM!--- QM
Symbol1

X1

Y1

Z1

XN

YN

ZN

...
SymbolN!--- MM
Symbol(N+1)

X(N+1)

Y(N+1)

X(N+M)

Y(N+M)

Z(N+1)

T...
Symbol(N+M)
End
TinXYZ!--- QM

Geom_ONIOM

Z(N+M)TMM

!1

Symbol1

X1

Y1

Z1

Param1

Bond1-1

Bond1-2

Bond1-3

SymbolN

XN

YN

ZN

ParamN

X(N+1)

Y(N+1)

Z(N+1)

Param(N+1)

Bond(N+1)-1

Y(N+M)

Z(N+M)

Param(N+M)

Bond(N+M)-1...
!N

BondN-1

BondN-2

BondN-3!--- MM
N+1

Symbol(N+1)

Bond(N+1)-2

Bond(N+1)-3...
N+M

Symbol(N+M)

Bond(N+M)-2End

X(N+M)

Bond(N+M)-3

ONIOM
NTChem

2-layer ONIOM

Molecular Mechanics
ONIOM

4Name.inp
NameLR.inp

Low-Real

NameLM.inp

Low-Model

NameHM.inp

High-Model

ONIOM

Geom

3

Prefix Name&ONIOM

NameLR = ’NameLR’

Low-Real

Prefix NameNameLM = ’NameLM’

Low-Model

Prefix Name

NameHM = ’NameHM’

High-RealPrefix NameLow-Real
Low-Real
ONIOM

Geom

Low-Model
Low-Model

Geom

Geom_ONIOM
T
Model

Geom

Geom_ONIOM
Symbol1

X1

Y1Z1

XN

YN

ZN

...
SymbolN

ModelT!--- Model part
Symbol(N+1)

X(N+1)

Y(N+1)

Z(N+1)

X(N+M)

Y(N+M)

T

Cap(N+1)

Scale(N+1)...
Symbol(N+M)

Z(N+M)

T

Cap(N+M)

Scale(N+M)

End
Molecular Mechanics

TinXYZModel
C 5H 82

Model

2

Geom_ONIOM
C-0.909200-1.126700-0.207500 T 2 0.7

C-1.300300

0.245100-0.107400

H-1.320900-2.040000-0.149000 TC-0.280000

1.163900-0.112100

H-2.149300

0.379500

0.806900

H-1.874700

0.435900-1.021500

H-0.214800

1.6641000.924700

H-0.164900

1.942400-0.794100

C

1.068700

0.180400-0.018000

H

1.688800

0.488300-0.918500

C

0.519000-1.207700-0.170000 T 9 0.7

H1.6621000.432500

0.911300

H

1.157900-2.003100-0.076500 TEnd
TinXYZ
1

C-0.909200-1.126700-0.207500

22311!2C-1.300300

0.245100-0.107400

1

1456

3

H

-1.320900-2.040000-0.149000

51!4C-0.280000

1.163900-0.112100

127

8

9!5

H

-2.149300

0.379500

0.806900

52!6H-1.874700

0.435900-1.021500

52

!7

H

-0.214800

1.6641000.924700

54!8H-0.164900

1.942400-0.794100

54!9C

1.068700

0.180400-0.018000

14!10

H

1.688800

0.488300-0.918500

5911

C

0.519000-1.207700-0.170000!12H

1.6621000.432500

0.911300

13H

1.157900-2.003100-0.076500

511

2159! Cap atom
2H-1.300300

0.245100-0.107400

519H

1.068700

0.180400-0.018000

511EndHigh-Model
High-Model

Low-Model

1011

913

12

DL-FindNudged Elastic Band

Dimer

Geom&DLFind

Coord.xyz	 
Cartesian
FixGeom(CoordType = 'Internal')

2

3

4

FixGeom
FixGeom!--- Fix bond length atom1 - atom2
atom1

atom2!--- Fix bond angle atom3 - atom4 - atom5
atom3

atom4

atom5!--- Fix dihedral angle atom6 - atom7 - atom8 - atom9
atom6

atom7

atom8

atom9

End
CartesianFixXYZ

CartesianCartesian
FixXYZ"X"FixXYZ!--- Fix X coordinate of atom1
atom1X!--- Fix X and Y coordinate of atom2
atom2(CoordType = 'XYZ')

XY!--- Fix X, Y and Z coordinate of atom3"Y""Z"

atom3XYZ

EndHessiangradient

HessianNudged Elastic Band (NEB)
NEB

NEB

2Name.inp
Neme.2nd.inp

Name.inp

Geom&DLFindName

NEB = .TRUE.

PrefixOtherGeom = 'Name.2nd'Geom
NEB

nebpath.xyz

NEB

nebinfoImage

XYZ

XYZ&DLFind
NInitImg- 1Image

Dimer
Dimer&DLFind

Dimer = .TRUE.

NEBPathNInitImg

Image
Image

Image
NImageImage
Image

&DLFindDump(dlf_*.chk)
Restart = .TRUE.

&DLFind¶º´µ¸´µ¼

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!!!!!6!!!!H!!!!!!1.218847!!!!0.419401!!!!1.501609!!!!!179!!!!!!!!4!
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!
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ONIOM(QM/MM)mùr(6)
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