I would like to scan a "bond" along an axis defined by the center of a ring and perpendicular to it. I defined my atomic structure, placed a dummy atom at the center of the ring and added the additional atom that is supposed to be scanned along the axis I defined above. I would like to perform a relaxed PES so I also constrain some (3) bond distances in the ring to keep its symmetry (using F). Now my problem is that the dummy atom is not counted in the indexes so I don't know how I can define the scan. Usually I would do "b 13 14 s 30 -0.1". I am not sure if this is possible. Thanks in advance for your comments. I attach the input file. Nicolas.
Yes, you can :). Please find the attached input file for scan the distance between H2O and Benzene. You can modify your input accordingly:
# HF/cc-pVDZ Opt(Z-matrix)
Benzol-H2O komplex
0 1
X
C 1 B1
C 1 B2 2 A1
C 3 B3 2 A2 1 D1
C 4 B4 3 A3 2 D2
C 5 B5 4 A4 2 D3
C 6 B6 5 A5 4 D4
H 2 B7 3 A6 1 D5
H 3 B8 2 A7 1 D6
H 4 B9 3 A8 1 D7
H 5 B10 4 A9 1 D8
H 6 B11 5 A10 1 D9
H 7 B12 6 A11 1 D10
O 1 B13 2 A12 3 D11
H 14 B14 1 A13 2 D12
H 14 B15 15 A14 2 D13
B1 1.46955690 F
B2 1.46955690 F
B3 1.46955690 F
B4 1.46955690 F
B5 1.46955690 F
B6 1.46955690 F
B7 1.09958690 F
B8 1.09958690 F
B9 1.09958690 F
B10 1.09958690 F
B11 1.09958690 F
B12 1.09958690 F
B13 8.00000000 S 11 -0.5
B14 0.96000000 F
B15 0.96000000 F
A1 60.00000000 F
A2 120.00000000 F
A3 120.00000000 F
A4 120.00000000 F
A5 120.00000000 F
A6 120.00000000 F
A7 120.00000000 F
A8 120.00000000 F
A9 120.00000000 F
A10 120.00000000 F
A11 120.00000000 F
A12 90.00000000 F
A13 109.50000000 F
A14 109.50000000 F
D1 0.00000000 F
D2 0.00000000 F
D3 0.00000000 F
D4 0.00000000 F
D5 180.00000000 F
D6 -180.00000000 F
D7 180.00000000 F
D8 180.00000000 F
D9 -180.00000000 F
D10 -180.00000000 F
D11 -90.00000000 F
D12 0.00000000 F
D13 0.00000000 F
Thanks for the answer. It seems in my case that only adding the scan in the bond/angle/dihedral definition doesn't work. Same for the frozen atoms, I need to put the "F" next to the definition AND also to add the bond/angle/dihedral definition at the end as shown in my input script. Am I the only one with this issue? Maybe the compiled version I am using is different? seems to be the gaussian09 D0.1
The trick is here is that you should start the numbering of atoms X. And of course you are not the only one who had been faced with this issue that's why I know this trick...:)
Allright thanks for your time Milan. Will rewrite the zmatrix or I will do it in cartesian by hand.
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