Z

1,2-DCE MD calculation

Trans

Gauchetrans DCE ab-initio cal.: in vacuum# P B3LYP/6-311+G** SCF=(Tight, MaxCycle=199) Pop=MK Opt=(Verytight)
Trans in vaccum
SCF Done: E(RB+HF-LYP) = -999.101195164 A.U.
Dipole moment (field-independent basis, Debye):
X= 0.0000 Y= 0.0000 Z= 0.0000 Tot= 0.0000
Charges from ESP fit,
Charge= 0.00000
Dipole= -0.0002 0.0004 0.0000 Tot= 0.0004
1 C -0.140250
2 C -0.147544
3 H 0.151597
4 H 0.151597
5 H 0.153429
6 H 0.153428
7 Cl -0.161613
8 Cl -0.160645--------------------------------------------------------------------Center Atomic Atomic
Coordinates (Angstroms)
Number Number
Type
X
Y
Z
--------------------------------------------------------------------1
6
0-2.666423 1.350983 0.000047
260-2.496026 -0.153972 -0.000044
31
0-3.185388 1.697689 -0.890453
41
0-3.185290 1.697593 0.890641
5
10-1.977159 -0.500583 -0.890638
6
10-1.977061 -0.500679 0.890457
7
17
0-1.028387 2.137183 -0.000001
817
0-4.134063 -0.940171 0.000004------------------------------------------------------------------------------------------------! Optimized Parameters !
! (Angstroms and Degrees) !
--------------------------------------------------! Name Definition
Value
Derivative Info.
-------------------------------------------------------------------------------! R1 R(1,2)
1.5146-DE/DX = 0.0! R2 R(1,3)
1.0874-DE/DX = 0.0! R3 R(1,4)
1.0874-DE/DX = 0.0! R4 R(1,7)
1.8169-DE/DX = 0.0! R5 R(2,5)
1.0874-DE/DX = 0.0! R6 R(2,6)
1.0874-DE/DX = 0.0! R7 R(2,8)
1.8169-DE/DX = 0.0! A1 A(2,1,3)
111.7432-DE/DX = 0.0! A2 A(2,1,4)
111.7432-DE/DX = 0.0! A3 A(2,1,7)
109.1796-DE/DX = 0.0! A4 A(3,1,4)
109.9579-DE/DX = 0.0! A5 A(3,1,7)
106.9936-DE/DX = 0.0! A6 A(4,1,7)
106.9937-DE/DX = 0.0! A7 A(1,2,5)
111.7432-DE/DX = 0.0! A8 A(1,2,6)
111.7432-DE/DX = 0.0! A9 A(1,2,8)
109.1796-DE/DX = 0.0! A10 A(5,2,6)
109.9579-DE/DX = 0.0! A11 A(5,2,8)
106.9936-DE/DX = 0.0! A12 A(6,2,8)
106.9936-DE/DX = 0.0! D1 D(3,1,2,5)
56.3113-DE/DX = 0.0! D2 D(3,1,2,6)-180.0-DE/DX = 0.0! D3 D(3,1,2,8)-61.8443-DE/DX = 0.0! D4 D(4,1,2,5)
180.0-DE/DX = 0.0! D5 D(4,1,2,6)-56.3113-DE/DX = 0.0! D6 D(4,1,2,8)
61.8443-DE/DX = 0.0! D7 D(7,1,2,5)-61.8443-DE/DX = 0.0! D8 D(7,1,2,6)
61.8444-DE/DX = 0.0! D9 D(7,1,2,8)-180.0-DE/DX = 0.0--------------------------------------------------------------------------------

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SCF Done: E(RB+HF-LYP) = -999.098668932

A.U.

gauche DCE ab-initio cal. :in vaccum

gauche - trans = 0.0687 eV = 798 K
trans : gaush = 14 : 1
Dipole moment (field-independent basis, Debye):
X= 0.0000 Y= 0.0000 Z= 2.9237 Tot= 2.9237---------------------------! Optimized Parameters !
! (Angstroms and Degrees) !
--------------------------------------------------! Name Definition
Value
Derivative Info.
-------------------------------------------------------------------------------! R1 R(1,2)
1.5117-DE/DX = 0.0! R2 R(1,3)
1.0881-DE/DX = 0.0! R3 R(1,4)
1.0907-DE/DX = 0.0! R4 R(1,7)
1.8095-DE/DX = 0.0! R5 R(2,5)
1.0881-DE/DX = 0.0! R6 R(2,6)
1.0907-DE/DX = 0.0! R7 R(2,8)
1.8095-DE/DX = 0.0! A1 A(2,1,3)
111.6849-DE/DX = 0.0! A2 A(2,1,4)
109.1663-DE/DX = 0.0! A3 A(2,1,7)
112.949-DE/DX = 0.0! A4 A(3,1,4)
109.554-DE/DX = 0.0! A5 A(3,1,7)
106.948-DE/DX = 0.0! A6 A(4,1,7)
106.3597-DE/DX = 0.0! A7 A(1,2,5)
111.6849-DE/DX = 0.0! A8 A(1,2,6)
109.1663-DE/DX = 0.0! A9 A(1,2,8)
112.949-DE/DX = 0.0! A10 A(5,2,6)
109.554-DE/DX = 0.0! A11 A(5,2,8)
106.948-DE/DX = 0.0! A12 A(6,2,8)
106.3597-DE/DX = 0.0! D1 D(3,1,2,5)
171.5295-DE/DX = 0.0! D2 D(3,1,2,6)-67.1696-DE/DX = 0.0! D3 D(3,1,2,8)50.9296-DE/DX = 0.0! D4 D(4,1,2,5)-67.1696-DE/DX = 0.0! D5 D(4,1,2,6)
54.1314-DE/DX = 0.0! D6 D(4,1,2,8)
172.2306-DE/DX = 0.0! D7 D(7,1,2,5)50.9296-DE/DX = 0.0! D8 D(7,1,2,6)
172.2306-DE/DX = 0.0! D9 D(7,1,2,8)-69.6702-DE/DX = 0.0--------------------------------------------------------------------------------

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--------------------------------------------------------------------Center Atomic Atomic
Coordinates (Angstroms)
Number Number
Type
X
Y
Z
--------------------------------------------------------------------1
6
0-0.412402 0.633448 0.896553
2600.412402 -0.633448 0.896553
310-1.476824 0.420231 0.821879
4
1
0-0.214921 1.189316 1.813985
5101.476824 -0.420231 0.821879
6
1
00.214921 -1.189316 1.813985
717
00.000319 1.744063 -0.471167
8
17
0-0.000319 -1.744063 -0.471167--------------------------------------------------------------------Charges from ESP fit, RMS= 0.00271 RRMS= 0.18267:
Charge= 0.00000
Dipole= 0.0011 -0.0006 3.0651 Tot= 3.0651
1 C -0.210818
2 C -0.187963
3 H 0.179542
4 H 0.161413
5 H 0.174044
6 H 0.156443
7 Cl -0.134562
8 Cl -0.138099

trans DCE ab-initio cal.: in DCE# P B3LYP/6-311+G** SCF=(Tight, MaxCycle=199) Pop=MK Opt=(Verytight) SCRF=(PCM,Solvent=DiChloroEthane)
Gauche DCE in DCE Variational PCM results=======================<psi(f)| H |psi(f)>(a.u.) = -999.100665<psi(f)|H+V(f)/2|psi(f)>(a.u.) = -999.105782
Total free energy in solution: with all non electrostatic terms(a.u.) = -999.102685-------------------------------------------------------------------(Polarized solute)-Solvent(kcal/mol) =-3.21-------------------------------------------------------------------Cavitation energy(kcal/mol) =10.82
Dispersion energy(kcal/mol) =-9.76
Repulsion energy(kcal/mol) =0.88
Total non electrostatic(kcal/mol) =1.94-------------------------------------------------------------------Dipole moment (field-independent basis, Debye):
X= 0.0000 Y= 0.0000 Z= 0.0008 Tot= 0.0008
Charges from ESP fit, RMS= 0.00279 RRMS= 0.25610:
Dipole= -0.0003 0.0010 0.0009 Tot= 0.0013
1 C -0.127995
2 C -0.133489
3 H 0.162514
4 H 0.162519
5 H 0.163971
6 H 0.163947
7 Cl -0.196074
8 Cl -0.195394
Center Atomic Atomic
Coordinates (Angstroms)
Number Number
Type
X
Y
Z
--------------------------------------------------------------------1
6
0-2.671814 1.349987 0.000121260-2.490634 -0.152978 -0.000002
31
0-3.184281 1.700475 -0.893659
41
0-3.183826 1.700541 0.894125
510-1.978231 -0.503369 -0.893854
610-1.978560 -0.503631 0.893931
717
0-1.027013 2.139935 -0.000343
817
0-4.135439 -0.942918 -0.000306------------------------------------------------------------------------------------------------! Optimized Parameters !
! (Angstroms and Degrees) !
--------------------------------------------------! Name Definition
Value
Derivative Info.
-------------------------------------------------------------------------------! R1 R(1,2)
1.5138-DE/DX = 0.0! R2 R(1,3)
1.0883-DE/DX = 0.0! R3 R(1,4)
1.0882-DE/DX = 0.0! R4 R(1,7)
1.8247-DE/DX = 0.0! R5 R(2,5)
1.0883-DE/DX = 0.0! R6 R(2,6)
1.0883-DE/DX = 0.0! R7 R(2,8)
1.8247-DE/DX = 0.0! A1 A(2,1,3)
112.0886-DE/DX = 0.0! A2 A(2,1,4)
112.0977-DE/DX = 0.0! A3 A(2,1,7)
108.7798-DE/DX = 0.0! A4 A(3,1,4)
110.4504-DE/DX = 0.0! A5 A(3,1,7)
106.5498-DE/DX = 0.0! A6 A(4,1,7)
106.5508-DE/DX = 0.0! A7 A(1,2,5)
112.091-DE/DX = 0.0! A8 A(1,2,6)
112.0954-DE/DX = 0.0! A9 A(1,2,8)
108.7795-DE/DX = 0.0! A10 A(5,2,6)
110.4504-DE/DX = 0.0! A11 A(5,2,8)
106.5534-DE/DX = 0.0! A12 A(6,2,8)
106.5474-DE/DX = 0.0! D1 D(3,1,2,5)
55.1532-DE/DX = 0.0! D2 D(3,1,2,6)-179.9754-DE/DX = 0.0! D3 D(3,1,2,8)-62.4135-DE/DX = 0.0! D4 D(4,1,2,5)-179.9755-DE/DX = 0.0! D5 D(4,1,2,6)-55.104-DE/DX = 0.0! D6 D(4,1,2,8)62.4579-DE/DX = 0.0! D7 D(7,1,2,5)-62.4078-DE/DX = 0.0! D8 D(7,1,2,6)
62.4637-DE/DX = 0.0! D9 D(7,1,2,8)-179.9745-DE/DX = 0.0--------------------------------------------------------------------------------

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gauche DCE ab-initio cal.: in DCE# P B3LYP/6-311+G** SCF=(Tight, MaxCycle=199) Pop=MK Opt=(Tight) SCRF=(PCM,Solvent=DiChloroEthane)
Trans in DCE Variational PCM results=====0.022 eV = 261.5 K trans : gauche = 1 : 0.42
<psi(f)| H |psi(f)><psi(f)|H+V(f)/2|psi(f)>Total free energy in solution:(a.u.) = -999.097322(a.u.) = -999.105161
with all non electrostatic terms(a.u.) = -999.101857-------------------------------------------------------------------(Polarized solute)-Solvent(kcal/mol) =-4.92-------------------------------------------------------------------Cavitation energy(kcal/mol) =10.84
Dispersion energy(kcal/mol) =-9.62
Repulsion energy(kcal/mol) =0.85
Total non electrostatic(kcal/mol) =2.07-------------------------------------------------------------------Dipole moment (field-independent basis, Debye):
X= 0.0000 Y= 0.0000 Z= 3.8279 Tot= 3.8279
Charges from ESP fit, RMS= 0.00262 RRMS= 0.13952:
Dipole= -0.0025 0.0003 3.9469 Tot= 3.9469
1 C -0.200412
2 C -0.180907
3 H 0.192555
4 H 0.186865
5 H 0.187347
6 H 0.182669
7 Cl -0.182611
8 Cl -0.185506--------------------------------------------------------------------Center Atomic Atomic
Coordinates (Angstroms)
Number Number
Type
X
Y
Z
--------------------------------------------------------------------1
6
0-0.413548 0.630461 0.902144
26
00.413548 -0.630461 0.902144
3
10-1.480490 0.424342 0.835481
41
0-0.201716 1.196748 1.810425
5101.480490 -0.424342 0.835481
6100.201716 -1.196748 1.810425
7
17
0-0.011466 1.736655 -0.487103
817
00.011466 -1.736655 -0.487103------------------------------------------------------------------------------------------------! Optimized Parameters !
! (Angstroms and Degrees) !
--------------------------------------------------! Name Definition
Value
Derivative Info.
!
-------------------------------------------------------------------------------! R1 R(1,2)
1.508-DE/DX = 0.0!
! R2 R(1,3)
1.0887-DE/DX = 0.0!
! R3 R(1,4)
1.0911-DE/DX = 0.0!
! R4 R(1,7)
1.8208-DE/DX = 0.0!
! R5 R(2,5)
1.0887-DE/DX = 0.0!
! R6 R(2,6)
1.0911-DE/DX = 0.0!
! R7 R(2,8)
1.8208-DE/DX = 0.0!
! A1 A(2,1,3)
112.2845-DE/DX = 0.0!
! A2 A(2,1,4)
109.1162-DE/DX = 0.0!
! A3 A(2,1,7)
112.7603-DE/DX = 0.0!
! A4 A(3,1,4)
109.8459-DE/DX = 0.0!
! A5 A(3,1,7)
106.5416-DE/DX = 0.0!
! A6 A(4,1,7)
106.0786-DE/DX = 0.0!
! A7 A(1,2,5)112.2845-DE/DX = 0.0!
! A8 A(1,2,6)
109.1162-DE/DX = 0.0!
! A9 A(1,2,8)
112.7603-DE/DX = 0.0!
! A10 A(5,2,6)
109.8459-DE/DX = 0.0!
! A11 A(5,2,8)
106.5416-DE/DX = 0.0!
! A12 A(6,2,8)106.0786-DE/DX = 0.0!
! D1 D(3,1,2,5)
172.4115-DE/DX = 0.0!
! D2 D(3,1,2,6)-65.5596-DE/DX = 0.0!
! D3 D(3,1,2,8)52.0396-DE/DX = 0.0!
! D4 D(4,1,2,5)-65.5596-DE/DX = 0.0!
! D5 D(4,1,2,6)
56.4693-DE/DX = 0.0!
! D6 D(4,1,2,8)
174.0685-DE/DX = 0.0!
! D7 D(7,1,2,5)
52.0396-DE/DX = 0.0!
! D8 D(7,1,2,6)
174.0685-DE/DX = 0.0!
! D9 D(7,1,2,8)-68.3322-DE/DX = 0.0!
--------------------------------------------------------------------------------

Basically you can make the potential from the quantum chemical (QC) calculation.
0) get the optimized structureintermolecular potential
1) it is better to use the QC cal. in the solvent (maybe!!)2) the electrostatic potential fit (ESP) charges can be used.
3) LJ potential can not obtained!! from QC cal.
the intra-moecular potential
4) bond length potential can be obtained from QC cal if the other degree of freedom is fixed.
5) bond angle potential can be obtained from QC cal if the other degree of freedom is fixed.
6) torsion angle potential can be obtained from QC cal if the other degree of freedom is fixed.
7) scaled intra-molecular 1-4 non-bonded interaction should be take into acount!

I will show the one example:
torsion angle potential Cl-C-C-Cl of DCE

Cl-C-C-Cl torsion angle potential of DCE in DCE

φtorsion angle dependence
for the structure of the trans configration
fully relaxed structure

0.6

8000

6000

0.4
4000

0.2

temperature / K

energy differnce / eV

0.8

2000

0.0

0
0

50

100

150

200

250

torsion angle / degree

300

350

exp: energy diff. trans- gauche in DCE 0.31 kcal mol-1 = 13.4 meV = 156 K cal. 262 Kin vacuum 1.20 kcal mol-1 = 52.0 meV = 604 K

cal. 798 K

OPLS-AA force field for 1,2-DCE

ClH2C-CH2Cl
C:12.011
H:1.0079
Cl:35.453
12.011×2 + 1.0079×4 + 35.453×2 =98.9596 g mol-1
1.2824 / 98.9596 = 0.012959 mol cm-3
= 0.007804 # Å-3
1 molecule = 128.14 Å3
256 molecules = 32803.74 Å3= (32.01163 Å)34×(4×4×4) = 256
32.01163 / 4 = 8.00291 Å

center of mass: fcc lattice
random orientation
crystalT. B. Reed and W. N. Lipscomb, Acta Cryst. 1953, 6, 45.

OPLS-AA force field
Ebond

=

!

bonds

Kr (r − req )2

k = 2Kr
OPLS:
optimized potentials
for liquid simulations
by W. L. Jorgensen et al.
AA: All-AtomOPLS-AA force field
Eangle=!

anglesKθ (θ − θeq )2

k = 2KθEtorsion (φi ) =OPLS-AA force field

when! "V i0i

2[1 + cos(f0i )]V1i+ [1 + cos(φi + f1i )]2V2i+ [1 − cos(2φi + f2i )]2#V3i+ [1 + cos(3φi + f3i )]2V0i , f0i , f1i , f2i , f3i = 0! "V i1[1 + cos(φi )]Etorsion (φi ) =2iV2i+ [1 − cos(2φi )]2#
V3i+ [1 + cos(3φi )]
2

→cos3

DCE all atom
units kJ
molecular types 1
DCE
nummols 1
atoms 8C
12.011-0.006 2H
1.00790.103 4Cl
35.4530-0.200 2
bonds 7
harm 1 3 2845.12 1.0900
harm 1 4 2845.12 1.0900
harm 2 5 2845.12 1.0900
harm 2 6 2845.12 1.0900
harm 1 2 2242.62 1.5290
harm 1 7 2050.16 1.7810
harm 2 8 2050.16 1.7810
angles 12
harm 1 2 5 313.8
110.70harm 1 2 6 313.8
110.70harm 2 1 3 313.8
110.70harm 2 1 4 313.8
110.70harm 3 1 4 276.1
107.80harm 5 2 6 276.1
107.80harm 1 2 8 577.4
109.80harm 2 1 7 577.4
109.80harm 3 1 7 426.8
107.60harm 4 1 7 426.8
107.60harm 5 2 8 426.8
107.60harm 6 2 8 426.8
107.60dihedrals 9
OPLS 3 1 2 5 0.00000 0.00000 0.0000 1.3305 0.5000
0.5000OPLS 3 1 2 6 0.00000 0.00000 0.0000 1.3305 0.5000
0.5000OPLS 4 1 2 5 0.00000 0.00000 0.0000 1.3305 0.5000
0.5000OPLS 4 1 2 6 0.00000 0.00000 0.0000 1.3305 0.5000
0.5000OPLS 3 1 2 8 0.00000 0.00000 0.0000 1.6736 0.5000
0.5000OPLS 4 1 2 8 0.00000 0.00000 0.0000 1.6736 0.5000
0.5000OPLS 5 2 1 7 0.00000 0.00000 0.0000 1.6736 0.5000
0.5000OPLS 6 2 1 7 0.00000 0.00000 0.0000 1.6736 0.5000
0.5000OPLS 7 1 2 8 1.046 -1.046 0.0000 0.0000 0.5000
0.5000finishvdw 6
CC lj 0.276144 3.5C
H lj 0.186176 3.0
C
Cl lj 0.588741 3.45
H
H lj 0.12552
2.5
H
Cl lj 0.396929 2.95
Cl
Cl lj 1.2552
3.4
close

FIELD

7

5
6

1

2

3
4

X

OPLS does not work!! Use cos3

8

Z

X

Please remember thatall bonds, angles, and torsion should bespecified. Otherwise, ↓DCE all atom
units kJ
molecular types 1
DCE
nummols 1
atoms 8C
12.011-0.006 2H
1.00790.103 4Cl
35.4530-0.200 2
bonds 3harm 1 3 2845.12 1.0900
harm 1 2 2242.62 1.5290
harm 1 7 2050.16 1.7810
angles 4
harm 1 2 5 313.8
110.70harm 3 1 4 276.1
107.80harm 1 2 8 577.4
109.80harm 3 1 7 426.8
107.60dihedrals 3
cos3 3 1 2 5 0.00000 0.0000 1.3305 0.5000 0.5000
cos3 3 1 2 8 0.00000 0.0000 1.6736 0.5000 0.5000
cos3 7 1 2 8 -1.046 0.0000 0.0000 0.5000 0.5000
finishvdw 6
CC lj 0.276144 3.5C
H lj 0.186176 3.0
C
Cl lj 0.588741 3.45
H
H lj 0.12552
2.5
H
Cl lj 0.396929 2.95
Cl
Cl lj 1.2552
3.4
close

after 30 fs

FIELD check cal.
structure relaxation of single moleculefrom all atom model potential
0 K, single molecule simulation
intra-molecule potential checkMD result: NVE 0.5 K, 1 molecule

cos3

5

7

2
6
3
1

8

4

bond / Angstrom
1-3 1.0910
1-4 1.0904
2-5 1.0916
2-6 1.0905
1-2 1.5314
1-7 1.7824
2-8 1.7829
angle / degree
125 111.37
126 111.30
213 111.26
214 111.44
314 108.03
526 108.27
128 110.06
217 110.13
317 107.83
417 108.02
528 107.71
628 108.00
torsion / degree3125 60.15
3126 181.07
4125 180.79
4126 301.71
3128 300.77
4128 61.40
5217 300.64
6217 61.56
7128 181.26

Cl-C-C-Cl torsion angle potential of DCE in DCE
FP cal. :from the structure of the trans configration
FP cal. :fully relaxed structure
MD force field

0.6

8000

6000

0.4
4000

0.2

temperature / K

energy differnce / eV

0.8

φ

2000

0.0

0
0

50

100

150

200

250

torsion angle / degree

300

350

exp: energy diff. trans- gauche in DCE 0.31 kcal mol-1 = 13.4 meV = 156 K cal. 262 Kin vacuum 1.20 kcal mol-1 = 52.0 meV = 604 K

cal. 798 K

57C-Cl bond length potential of DCE in DCE
2
6
3
1

8

4

C-Cl bond of trans 1,2-DCE

3

25x10

FP cal.
MD force field

1.5

20

15
1.0
10

0.5

5

0.0

0
1.6

1.8
C-Cl bond length / Angstrom

2.0

2.2

temperrature / K

energy difference / eV

2.0

5

7

C-C-Cl bond anglel potential of DCE in DCE
2
6
3
1

8

DCE C-C-Cl angle

1.4

3

16x10
14

1.2
FP cal.
MD force field

12

1.0

10
0.8
8
0.6
6
0.4

4

0.2

2

0.0

0
80

90

100

110
120
C-C-Cl angle / degree

130

140

temperature / K

energy / eV

4

Now we move to 356 mol. system.
initial configuration

NVE simulation: results
self-diffusion
run terminated after 1500000 steps. final averages calculated over 1000000 steps.

DCE NVE 256 mol.
----------------------------------------------------------------------------------------------------------------------------------

integrator velocity verlet
temperature
300.0
ensemble nve
steps
1500000
equilibration 500000
multiple step
1
scale
10
print
50
stack
100
stats
10
rdf
1
traj 1 100 0
timestep
0.0001
cutoff9.50
delr width
0.5000ewald precision 1d-6
shake tolerance 1.0E-5
quaternion tolerance 1.0E-5
print rdf
job timeclose timefinish300000.00
1000.00

step eng_tot temp_tot eng_cfg eng_vdw
time(ps)
eng_pv temp_rot vir_cfg vir_vdw
cpu (s)volume temp_shl eng_shl vir_shl

eng_cou eng_bnd eng_ang eng_dih eng_tet
vir_cou vir_bnd vir_ang vir_con vir_tet
alpha
beta
gamma vir_pmf
press---------------------------------------------------------------------------------------------------------------------------------1500000 4.3299E+03 3.0077E+02 -3.3486E+03 -6.8950E+03 -1.9603E+03 2.1842E+03 3.1003E+03 2.2218E+02 0.0000E+00
150.000 6.4082E+03 0.0000E+00 9.1222E+03 -6.5921E+03 1.9600E+03 1.3754E+04 0.0000E+00 0.0000E+00 0.0000E+00******** 3.2791E+04 0.0000E+00 0.0000E+00 0.0000E+00 9.0000E+01 9.0000E+01 9.0000E+01 0.0000E+00 1.0387E+00
r.m.s. 5.2674E-01 3.8798E+00 9.9063E+01 6.7939E+01 6.0573E+01 7.0591E+01 9.4880E+01 3.2248E+01 0.0000E+00
fluctn. 1.5009E+03 0.0000E+00 4.5155E+03 1.1320E+03 6.0584E+01 4.2374E+03 0.0000E+00 0.0000E+00 0.0000E+00
0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 7.5013E-01---------------------------------------------------------------------------------------------------------------------------------Approximate 3D Diffusion coefficients (10^-9 m^2 / s)
atom
C
H
Cl

D
1.0027E+00
9.9311E-01
1.0486E+00

Average pressure tensor
1.0153E+00 -2.7400E-02 -7.6797E-03-2.7400E-02 1.0548E+00 1.1290E-02-7.6797E-03 1.1290E-02 1.0460E+00

r.m.s. fluctuations
1.1143E+00 7.1434E-01 7.1722E-01
7.1434E-01 1.0973E+00 6.9323E-01
7.1722E-01 6.9323E-01 1.1083E+00

trace/3. 1.0387E+00

Self-diffusion const. of 1,2-DCE 1.692E-9 m2 s-1 298.15 K 0.1 MPa
0.985E-9 m2 s-1 298.15 100.8 MPa
rho 1245.98 kg m-3 at 298.15 K
R. Malhotra, W. E. Price, L. A. Woolf and A. J. Easteal
Thermodynamic and transport properties of 1, 2-dichloroethaneInternational Journal of Thermophysics
Volume 11, Number 5 / 1990年9月 835-861

NVE simulation:
RDF
1.4

radial distribution function

1.2

1.0

0.8

0.6

0.4

C-C
Cl - Cl

0.2

0.0
3

4

5

6
7
distance / Angstrom

89

NVE simulation: animation

NPT simulation: results
DCE NVE 256 mol.
integrator velocity verlet
temperature
300.0
ensemble npt hoover 0.1 0.2
steps
1500000
equilibration 500000
multiple step
1
scale
10
print
50
stack
100
stats
10
rdf
1
traj 1 100 0
timestep
0.0001
cutoff9.50
delr width
0.5000ewald precision 1d-6
shake tolerance 1.0E-5
quaternion tolerance 1.0E-5
print rdf
pres 0.001

run terminated after 1500000 steps. final averages calculated over 1000000 steps.
---------------------------------------------------------------------------------------------------------------------------------step eng_tot temp_tot eng_cfg eng_vdw eng_cou eng_bnd eng_ang eng_dih eng_tettime(ps)
eng_pv temp_rot vir_cfg vir_vdw vir_cou vir_bnd vir_ang vir_con vir_tet
cpu (s)volume temp_shl eng_shl vir_shl
alpha
beta
gamma vir_pmf
press---------------------------------------------------------------------------------------------------------------------------------1500000 5.6388E+03 3.0000E+02 -2.6014E+03 -6.1940E+03 -1.7966E+03 2.1290E+03 3.0296E+03 2.3051E+02 0.0000E+00
150.000 5.0597E+03 0.0000E+00 1.5311E+04 -3.3301E+03 1.7958E+03 1.6845E+04 0.0000E+00 0.0000E+00 0.0000E+00******** 3.6001E+04 0.0000E+00 0.0000E+00 0.0000E+00 9.0000E+01 9.0000E+01 9.0000E+01 0.0000E+00 2.1809E-03
r.m.s. 5.8095E+01 5.4122E+00 2.4561E+02 2.1253E+02 9.3930E+01 9.5145E+01 9.6932E+01 3.4834E+01 0.0000E+00
fluctn. 1.5768E+03 0.0000E+00 4.6418E+03 1.0358E+03 9.4067E+01 4.4672E+03 0.0000E+00 0.0000E+00 0.0000E+00
9.1542E+02 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 7.0717E-01----------------------------------------------------------------------------------------------------------------------------------

Approximate 3D Diffusion coefficients (10^-9 m^2 / s)
atom
C
H
Cl

D
2.2328E+00
2.2248E+00
2.2788E+00

Average pressure tensor

r.m.s. fluctuations-1.0661E-02 1.2868E-02 -1.3885E-03
1.2868E-02 2.1396E-02 2.8010E-03-1.3885E-03 2.8010E-03 -4.1919E-03
trace/3. 2.1809E-03
Average cell vectors

job timeclose timefinish300000.00
1000.00

1.0312E+00 6.2499E-01 6.3513E-01
6.2499E-01 1.0251E+00 6.3548E-01
6.3513E-01 6.3548E-01 1.0273E+00

33.0171898095.0000000000.0000000000.0000000000
33.0171898095.0000000000

r.m.s. fluctuations.0000000000.0000000000
33.0171898095

2.7817E-01 0.0000E+00 0.0000E+00
0.0000E+00 2.7817E-01 0.0000E+00
0.0000E+00 0.0000E+00 2.7817E-01

rho_cal: 1168.8 kg m-3
Self-diffusion const. of 1,2-DCE 1.692E-9 m2 s-1 298.15 K 0.1 MPa
0.985E-9 m2 s-1 298.15 100.8 MPa
rho 1245.98 kg m-3 at 298.15 K
R. Malhotra, W. E. Price, L. A. Woolf and A. J. Easteal
Thermodynamic and transport properties of 1, 2-dichloroethaneInternational Journal of Thermophysics
Volume 11, Number 5 / 1990年9月 835-861

NPT simulation

1.4

radial distribution function

1.2
1.0
0.8
0.6

C-C
Cl - Cl

0.4
0.2
0.0
3

4

5

6
7
distance / Angstrom

89

NPT simulation

This is the end of thetutorial.
I hope now you can start tosimulate the system thatyou have interest.

One more very important thing!!
You can find the force field parameter
sets from the following site.
ftp://dasher.wustl.edu/pub/tinker/params
You can get Amber, OPLS-AA, Charmm,
Dang and etc.

Thank you for your attention.
Good luck!!

2007/08/23 M. Y.