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I'm trying to do a redundant PES scan of a hydrogen abstraction in a Gaussian job while maintaining the rest of the system fixed. I need to scan the coordinate where H5 approaches to H6, maintaining the rest of the methane in place (that is, increasing the C1 H5 bond length). When I do a scan, the H6 just approaches H5. Is there a way so I can freeze everything except the coordinates of H5? So the distance between C1 and H5 increases and the distance between H5 and H6 decreases.
I think @romaichenko's answer covers everything. But for a full answer I believe a sample input file is necessary.
# B3LYP/6-31G(d) Opt=ModRedundant
methane with H
0 2
C -1.41531 0.37839 0.00000
H -0.34531 0.37839 0.00000
H -1.77197 0.64640 -0.97255
H -1.77198 1.08664 0.71838
H -1.77198 -0.59787 0.25418
H -2.67803 -3.10703 0.79353
B 1 6 F
B 5 6 S 20 -0.1
! there has to be a newline at the end of input file
Here, replace the coordinates and the charge/multiplicity with your own coordinates. If you want atom 5 to move while keeping atom 1 and atom 6 fixed, then you would have to fix the distance between 1 and 6. B indicates bond and F requests Gaussian to freeze that coordinate.
The last line indicates that the bond (B) between atoms 5 and 6 are scanned (S) with 20 steps of size -0.1 Angstrom. In the image you posted in the question, the bond between 5 and 6 is long, so during the scan, the bond length would have to decrease which is why the step size is negative. Make sure that the number of the scan steps and the step size are consistent with the bond lengths of your system, because I cannot say what is the distance between 5 and 6 from an image. 20 steps of step size -0.1 Angstrom will reduce the bond length by 2 Angstrom.
Note that the coordinates of the other three H atoms on methyl group (2,3,4) are not frozen, so they can move during the optimization, i.e. this is a relaxed scan to some extent.
X 1 F and X 6 F, and then put B 1 6 F before the B 5 6 S 20 -0.1 line. ( I have edited my answer with this)
$\endgroup$
Jun 20, 2021 at 12:13
It can be done using ModRedundant option in Gaussian (more on that here). You just freeze everything in space except for the 5th and 6th hydrogen.
However, in my opinion it would be better to perform a so called relaxed scan (a series of optimizations with the scanned coordinate fixed to certain values) as it yields better geometries for system states during the reaction.
