enter image description hereHow can i displace my structure along a particular normal mode, without coupling to other modes ? Rather than a exact mathematical procedure, I am more interested in a software/script/package that can help me accomplish it.

For the kind of computations I am doing just displacing along modes in cartesians isn't accurate because modes involving bending and angles lead to bond stretching. For example,the descriptin of rotational mode of methyl group in cartesian cant be used for displacements as it leads to stretching of CH bonds

I have a pseudo-process in my mind. A frequency computation in Gaussian gives me the normal modes in both cartesian displacements and redundant internals. My aim is to displacement along modes in redundant internals and then back-transform to cartesian coordinates. I beleive this should be possible as Gaussain must store the transforming matrixes somewhere( after all, it does this during optimizations), but I have not been able to accomplish this even after rummagging through all iops.

More importantly, I think this kind of task is quite standard (for decades !) and there surely must be an efficient way to do this.

So, If anyone here can advise me or point me towards the right direction.

  • $\begingroup$ Comments are not for extended discussion; this conversation has been moved to chat. $\endgroup$ – Tyberius Apr 13 at 14:32

Well, I found a dirty way to do with Gaussian itself. I make the computtaion print the normal modes in redundant internals with IntModes option.

To displace the structure along the normal modes in redundant internals, I use the GIC section and manually specify the values of the redundant internals. Then I submit a pseudo-computaion(hf/sto-3G) to gaussian.

Before doing the computtaion gaussian prints the displaced structure in Cartesians.

I still feel this is quite ugly, and there must be a proper way to accomplish this.


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