Hi
I am modeling Azobenzene with all atoms method.
The following paper shows the complete force field BONDED parameters for the azobenzene compound with GROMACS packages.
I am using their force field parameters in my simulation and trying to reproduce their results which are shown on Fig 2 and Fig 3 in the paper.
IMPROPER and NONBONDED force field parameters are not modified in my simulation simply using AMBER DEFAULT values.
My simulation is in gas phase 300K, so I think non-bonded parameters are not quite important.
Unfortunately, I could NOT get the same results as they did.
Are AMBER and GROMOS force field parameters compatible???
Or, I have made some mistakes???
My .frcmod file and my .prmtop file are shown as follows.
Thanks
Lin
trans-azobenzene--their results
CNNC (180 +-15 degree)
CCNN ( 0 +- 30 degree)
trans-azobenzene--my results
CNNC (180 +-15 degree)
CCNN (the two phenyl rings can rotate freely ; most of time vibrate 0 +- 30 degrees or 120+-30 degrees)
cis-azobenzene--their results
CNNC (-10 +- 20 degree)
CCNN ( -52 +- 17 degree)
cis-azobenzene--my results
CNNC ( 0+- 20 degree)
CCNN ( the two phenyl rings can rotate freely ; most of time vibrate -60+- 30 degrees or 120+-30 degrees)
http://pubs.acs.org/cgi-bin/abstract.cgi/jctcce/2007/3/i05/abs/ct7000733.html
J. Chem. Theory Comput., 3 (5), 1789 -1802, 2007. 10.1021/ct7000733
Atomistic Force Field for Azobenzene Compounds Adapted for QM/MM Simulations with Applications to Liquids and Liquid Crystals
TABLE 2. Nonstandard Force Field Parameters Derived for Azobenzene
force constant trans cis
bonds: NN 1.40*10^3 kJ/mol 1.270 Angstrons 1.255 Angstrons
CN 0.72*10^3kJ/mol 1.425 Angstrons 1.440 Angstrons
angles: CNN 650.0 kJ/mol 114 degrees 119 degrees
CCN 560.0 kJ/mol 120 degrees 120 degrees
dihedrals: CNNC 70.0 kJ/mol 180 degrees 180 degrees
CCNN 6.0 kJ/mol 180 degrees 180 degrees
XCCX 40.0 kJ/mol 180 degrees 180 degrees
point charges: N -0.2e -0.2e
C1 0.2e 0.2e
C2-C6 -0.1e -0.1e
H 0.1e 0.1e
remark goes here
MASS
BOND
ne-nf 334.61 1.255
ca-ne 172.08 1.440
ca-nf 172.08 1.440
ca-ha 293.98 1.09
ca-ca 258.13 1.39
ANGLE
ca-ne-nf 155.35 119.0
ca-nf-ne 155.35 119.0
ca-ca-ne 133.84 120.0
ca-ca-nf 133.84 120.0
ca-ca-ca 133.84 120.0
ca-ca-ha 120.67 120.0
DIHE
ca-ne-nf-ca 2 33.46 180 2.0
ca-nf-ne-ca 2 33.46 180 2.0
ca-ca-ne-nf 2 2.87 180 2.0
ca-ca-nf-ne 2 2.87 180 2.0
ne-nf-ca-ca 2 2.87 180 2.0
nf-ne-ca-ca 2 2.87 180 2.0
ca-ca-ca-ca 2 19.12 180 2.0
ha-ca-ca-ha 2 19.12 180 2.0
ca-ca-ca-ha 2 19.12 180 2.0
ha-ca-ca-ca 2 19.12 180 2.0
ha-ca-ca-ne 2 19.12 180 2.0
ne-ca-ca-ha 2 19.12 180 2.0
ha-ca-ca-nf 2 19.12 180 2.0
nf-ca-ca-ha 2 19.12 180 2.0
ca-ca-ca-ne 2 19.12 180 2.0
ne-ca-ca-ca 2 19.12 180 2.0
ca-ca-ca-nf 2 19.12 180 2.0
nf-ca-ca-ca 2 19.12 180 2.0
IMPROPER
ca-ca-ca-ha 1.1 180.0 2.0 General improper torsional angle (2 general atom types)
ca-ca-ca-ne 1.1 180.0 2.0 Using default value
ca-ca-ca-nf 1.1 180.0 2.0 Using default value
RDPARM MENU: atom
Mask [] represents 24 atoms
Number: Atom Charge Mass ( Residue ) Type Tree
1: C3 -0.10000 12.0 ( 1:MOL ) ca M
2: H3 0.10000 1.0 ( 1:MOL ) ha E
3: C2 -0.10000 12.0 ( 1:MOL ) ca B
4: H2 0.10000 1.0 ( 1:MOL ) ha E
5: C1 -0.10000 12.0 ( 1:MOL ) ca B
6: H1 0.10000 1.0 ( 1:MOL ) ha E
7: C6 -0.10000 12.0 ( 1:MOL ) ca B
8: H5 0.10000 1.0 ( 1:MOL ) ha E
9: C5 -0.10000 12.0 ( 1:MOL ) ca S
10: H4 0.10000 1.0 ( 1:MOL ) ha E
11: C4 0.20000 12.0 ( 1:MOL ) ca M
12: N1 -0.20000 14.0 ( 1:MOL ) ne M
13: N2 -0.20000 14.0 ( 1:MOL ) nf M
14: C7 0.20000 12.0 ( 1:MOL ) ca M
15: C8 -0.10000 12.0 ( 1:MOL ) ca B
16: H6 0.10000 1.0 ( 1:MOL ) ha E
17: C9 -0.10000 12.0 ( 1:MOL ) ca B
18: H7 0.10000 1.0 ( 1:MOL ) ha E
19: C10 -0.10000 12.0 ( 1:MOL ) ca B
20: H8 0.10000 1.0 ( 1:MOL ) ha E
21: C11 -0.10000 12.0 ( 1:MOL ) ca S
22: H9 0.10000 1.0 ( 1:MOL ) ha E
23: C12 -0.10000 12.0 ( 1:MOL ) ca M
24: H10 0.10000 1.0 ( 1:MOL ) ha E
RDPARM MENU: angles
Mask [] represents 24 atoms
Angle Kthet degrees atom names (numbers)
1: 120.670 120.00 :1.C3 :1.C2 :1.H2 (1,3,4)
2: 120.670 120.00 :1.H3 :1.C3 :1.C2 (2,1,3)
3: 120.670 120.00 :1.H3 :1.C3 :1.C4 (2,1,11)
4: 120.670 120.00 :1.C2 :1.C1 :1.H1 (3,5,6)
5: 120.670 120.00 :1.H2 :1.C2 :1.C1 (4,3,5)
6: 120.670 120.00 :1.C1 :1.C6 :1.H5 (5,7,8)
7: 120.670 120.00 :1.H1 :1.C1 :1.C6 (6,5,7)
8: 120.670 120.00 :1.C6 :1.C5 :1.H4 (7,9,10)
9: 120.670 120.00 :1.H5 :1.C6 :1.C5 (8,7,9)
10: 120.670 120.00 :1.H4 :1.C5 :1.C4 (10,9,11)
11: 120.670 120.00 :1.C7 :1.C8 :1.H6 (14,15,16)
12: 120.670 120.00 :1.C7 :1.C12 :1.H10 (14,23,24)
13: 120.670 120.00 :1.C8 :1.C9 :1.H7 (15,17,18)
14: 120.670 120.00 :1.H6 :1.C8 :1.C9 (16,15,17)
15: 120.670 120.00 :1.C9 :1.C10 :1.H8 (17,19,20)
16: 120.670 120.00 :1.H7 :1.C9 :1.C10 (18,17,19)
17: 120.670 120.00 :1.C10 :1.C11 :1.H9 (19,21,22)
18: 120.670 120.00 :1.H8 :1.C10 :1.C11 (20,19,21)
19: 120.670 120.00 :1.C11 :1.C12 :1.H10 (21,23,24)
20: 120.670 120.00 :1.H9 :1.C11 :1.C12 (22,21,23)
21: 133.840 120.00 :1.C3 :1.C2 :1.C1 (1,3,5)
22: 133.840 120.00 :1.C3 :1.C4 :1.C5 (1,11,9)
23: 133.840 120.00 :1.C3 :1.C4 :1.N1 (1,11,12)
24: 133.840 120.00 :1.C2 :1.C3 :1.C4 (3,1,11)
25: 133.840 120.00 :1.C2 :1.C1 :1.C6 (3,5,7)
26: 133.840 120.00 :1.C1 :1.C6 :1.C5 (5,7,9)
27: 133.840 120.00 :1.C6 :1.C5 :1.C4 (7,9,11)
28: 133.840 120.00 :1.C5 :1.C4 :1.N1 (9,11,12)
29: 155.350 119.00 :1.C4 :1.N1 :1.N2 (11,12,13)
30: 155.350 119.00 :1.N1 :1.N2 :1.C7 (12,13,14)
31: 133.840 120.00 :1.N2 :1.C7 :1.C8 (13,14,15)
32: 133.840 120.00 :1.N2 :1.C7 :1.C12 (13,14,23)
33: 133.840 120.00 :1.C7 :1.C8 :1.C9 (14,15,17)
34: 133.840 120.00 :1.C7 :1.C12 :1.C11 (14,23,21)
35: 133.840 120.00 :1.C8 :1.C7 :1.C12 (15,14,23)
36: 133.840 120.00 :1.C8 :1.C9 :1.C10 (15,17,19)
37: 133.840 120.00 :1.C9 :1.C10 :1.C11 (17,19,21)
38: 133.840 120.00 :1.C10 :1.C11 :1.C12 (19,21,23)
RDPARM MENU: dihedrals
Mask [] represents 24 atoms
Dihedral pk phase pn atoms
1: 9.560 3.14 2.0 :1.C3 :1.C2 :1.C1 :1.H1 (1,3,5,6)
2: 9.560 3.14 2.0 :1.C3 :1.C4 :1.C5 :1.H4 (1,11,9,10)
3: 9.560 3.14 2.0 :1.H3 :1.C3 :1.C2 :1.H2 (2,1,3,4)
4: 9.560 3.14 2.0 :1.H3 :1.C3 :1.C2 :1.C1 (2,1,3,5)
5: 9.560 3.14 2.0 :1.H3 :1.C3 :1.C4 :1.C5 (2,1,11,9)
6: 9.560 3.14 2.0 :1.H3 :1.C3 :1.C4 :1.N1 (2,1,11,12)
7: 9.560 3.14 2.0 :1.C2 :1.C1 :1.C6 :1.H5 (3,5,7,8)
8: 9.560 3.14 2.0 :1.C4 :1.C3 :1.C2 :1.H2 (11,1,3,4)
9: 9.560 3.14 2.0 :1.H2 :1.C2 :1.C1 :1.H1 (4,3,5,6)
10: 9.560 3.14 2.0 :1.H2 :1.C2 :1.C1 :1.C6 (4,3,5,7)
11: 9.560 3.14 2.0 :1.C1 :1.C6 :1.C5 :1.H4 (5,7,9,10)
12: 9.560 3.14 2.0 :1.H1 :1.C1 :1.C6 :1.H5 (6,5,7,8)
13: 9.560 3.14 2.0 :1.H1 :1.C1 :1.C6 :1.C5 (6,5,7,9)
14: 9.560 3.14 2.0 :1.H5 :1.C6 :1.C5 :1.H4 (8,7,9,10)
15: 9.560 3.14 2.0 :1.H5 :1.C6 :1.C5 :1.C4 (8,7,9,11)
16: 9.560 3.14 2.0 :1.H4 :1.C5 :1.C4 :1.N1 (10,9,11,12)
17: 9.560 3.14 2.0 :1.N2 :1.C7 :1.C8 :1.H6 (13,14,15,16)
18: 9.560 3.14 2.0 :1.N2 :1.C7 :1.C12 :1.H10 (13,14,23,24)
19: 9.560 3.14 2.0 :1.C7 :1.C8 :1.C9 :1.H7 (14,15,17,18)
20: 9.560 3.14 2.0 :1.C7 :1.C12 :1.C11 :1.H9 (14,23,21,22)
21: 9.560 3.14 2.0 :1.C8 :1.C7 :1.C12 :1.H10 (15,14,23,24)
22: 9.560 3.14 2.0 :1.C8 :1.C9 :1.C10 :1.H8 (15,17,19,20)
23: 9.560 3.14 2.0 :1.H6 :1.C8 :1.C7 :1.C12 (16,15,14,23)
24: 9.560 3.14 2.0 :1.H6 :1.C8 :1.C9 :1.H7 (16,15,17,18)
25: 9.560 3.14 2.0 :1.H6 :1.C8 :1.C9 :1.C10 (16,15,17,19)
26: 9.560 3.14 2.0 :1.C9 :1.C10 :1.C11 :1.H9 (17,19,21,22)
27: 9.560 3.14 2.0 :1.H7 :1.C9 :1.C10 :1.H8 (18,17,19,20)
28: 9.560 3.14 2.0 :1.H7 :1.C9 :1.C10 :1.C11 (18,17,19,21)
29: 9.560 3.14 2.0 :1.C10 :1.C11 :1.C12 :1.H10 (19,21,23,24)
30: 9.560 3.14 2.0 :1.H8 :1.C10 :1.C11 :1.H9 (20,19,21,22)
31: 9.560 3.14 2.0 :1.H8 :1.C10 :1.C11 :1.C12 (20,19,21,23)
32: 9.560 3.14 2.0 :1.H9 :1.C11 :1.C12 :1.H10 (22,21,23,24)
B 33: 1.100 3.14 2.0 :1.H3 :1.C3 :1.C4 :1.C2 (2,1,11,3)
B 34: 1.100 3.14 2.0 :1.C3 :1.C1 :1.C2 :1.H2 (1,5,3,4)
B 35: 1.100 3.14 2.0 :1.C2 :1.C6 :1.C1 :1.H1 (3,7,5,6)
B 36: 1.100 3.14 2.0 :1.C1 :1.C5 :1.C6 :1.H5 (5,9,7,8)
B 37: 1.100 3.14 2.0 :1.C6 :1.C4 :1.C5 :1.H4 (7,11,9,10)
B 38: 1.100 3.14 2.0 :1.C7 :1.C9 :1.C8 :1.H6 (14,17,15,16)
B 39: 1.100 3.14 2.0 :1.C8 :1.C10 :1.C9 :1.H7 (15,19,17,18)
B 40: 1.100 3.14 2.0 :1.C9 :1.C11 :1.C10 :1.H8 (17,21,19,20)
B 41: 1.100 3.14 2.0 :1.C10 :1.C12 :1.C11 :1.H9 (19,23,21,22)
B 42: 1.100 3.14 2.0 :1.C7 :1.C11 :1.C12 :1.H10 (14,21,23,24)
43: 9.560 3.14 2.0 :1.C3 :1.C2 :1.C1 :1.C6 (1,3,5,7)
E 44: 9.560 3.14 2.0 :1.C3 :1.C4 :1.C5 :1.C6 (1,11,9,7)
45: 1.435 3.14 2.0 :1.C3 :1.C4 :1.N1 :1.N2 (1,11,12,13)
46: 9.560 3.14 2.0 :1.C2 :1.C3 :1.C4 :1.C5 (3,1,11,9)
47: 9.560 3.14 2.0 :1.C2 :1.C3 :1.C4 :1.N1 (3,1,11,12)
E 48: 9.560 3.14 2.0 :1.C2 :1.C1 :1.C6 :1.C5 (3,5,7,9)
49: 9.560 3.14 2.0 :1.C4 :1.C3 :1.C2 :1.C1 (11,1,3,5)
E 50: 9.560 3.14 2.0 :1.C1 :1.C6 :1.C5 :1.C4 (5,7,9,11)
51: 9.560 3.14 2.0 :1.C6 :1.C5 :1.C4 :1.N1 (7,9,11,12)
52: 1.435 3.14 2.0 :1.C5 :1.C4 :1.N1 :1.N2 (9,11,12,13)
53: 16.730 3.14 2.0 :1.C4 :1.N1 :1.N2 :1.C7 (11,12,13,14)
54: 1.435 3.14 2.0 :1.N1 :1.N2 :1.C7 :1.C8 (12,13,14,15)
55: 1.435 3.14 2.0 :1.N1 :1.N2 :1.C7 :1.C12 (12,13,14,23)
56: 9.560 3.14 2.0 :1.N2 :1.C7 :1.C8 :1.C9 (13,14,15,17)
57: 9.560 3.14 2.0 :1.N2 :1.C7 :1.C12 :1.C11 (13,14,23,21)
58: 9.560 3.14 2.0 :1.C7 :1.C8 :1.C9 :1.C10 (14,15,17,19)
E 59: 9.560 3.14 2.0 :1.C7 :1.C12 :1.C11 :1.C10 (14,23,21,19)
60: 9.560 3.14 2.0 :1.C8 :1.C7 :1.C12 :1.C11 (15,14,23,21)
E 61: 9.560 3.14 2.0 :1.C8 :1.C9 :1.C10 :1.C11 (15,17,19,21)
62: 9.560 3.14 2.0 :1.C9 :1.C8 :1.C7 :1.C12 (17,15,14,23)
E 63: 9.560 3.14 2.0 :1.C9 :1.C10 :1.C11 :1.C12 (17,19,21,23)
B 64: 1.100 3.14 2.0 :1.C3 :1.C5 :1.C4 :1.N1 (1,9,11,12)
B 65: 1.100 3.14 2.0 :1.C8 :1.C12 :1.C7 :1.N2 (15,23,14,13)
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Received on Sun May 11 2008 - 06:07:16 PDT
