11
$\begingroup$

This is related to a prior question of mine Derivatives with respect to user defined vibrational modes. While that one focuses on potential software to use for derivatives with respect to normal modes, I want to present the actual problem that led me to that.

I have the derivatives of some property $P$ with respect to the $3N-6=M$ normal vibrational modes $\big\{Q_i\big\}$ of a molecule. I wanted to convert these modes to a local mode basis to more directly relate these derivatives to functional groups of the molecule. Conversion of the modes to a local basis can done by a simple unitary transformation [1]: $$\mathbf{Q}'=\mathbf{QU}$$ Here, $\mathbf{Q}$ is a $3N\times M$ matrix of the normal modes, $\mathbf{U}$ is $M\times M$ unitary matrix defined via an iterative process described in the linked paper, and $\mathbf{Q'}$ is a matrix of the normal modes.

With the modes transformed, I also want derivatives in this local mode basis. I have two ways of doing this:

  • Transform the original derivatives: $\frac{\partial P}{\partial Q_i'}=\sum_jU_{ji}\frac{\partial P}{\partial Q_i}$ where the derivatives are arranged as column vectors.
  • Compute numerical derivatives along the new mode: $\frac{P(X+hQ_i')-P(X)}{h|Q_i'|}$ where $X$ is the initial molecule geometry.

However, the transformed derivatives and the numerical derivatives of the local modes do not seem to match. If I test my procedure on the normal modes, the numerical derivatives agree with the ones I get from Gaussian. I'm concerned that perhaps I have something mixed up with removing/keeping the mass weighting of the modes (Gaussian fiddles with the coordinate representation a lot during vibrational analysis). Is there something obviously wrong with the procedure I have outlined above? Can I transform mass-weighted normal modes properly or do I need to ensure they are in cartesian coordinates before performing the transformation?

  1. Jacob, C.R & Reiher, M. J. Chem. Phys. 130, 084106 (2009); DOI: 10.1063/1.3077690
$\endgroup$
  • $\begingroup$ I just want to be clear: your problem is that taking the derivative and then doing the transformation is not giving you the same result at doing the transformation and then taking the derivative? $\endgroup$ – taciteloquence May 21 at 2:43
  • $\begingroup$ @taciteloquence basically, yes. I have the derivatives from outputted from a Gaussian calculation, as well as the normal modes themselves. If I transform the derivatives, I get a different result then if I transform the modes and recompute the derivatives. $\endgroup$ – Tyberius May 21 at 3:27
  • $\begingroup$ I wonder if "numerical-convergence" might be appropriate here? It's not exactly talking about numerical-convergence like in the sense of SCF, but there's a numerical discrepancy between derivatives calculated numerically, so people "watching" the convergence tag might be interested. The people interested in "scientific computation" or "numerical techniques" might be interested. $\endgroup$ – Nike Dattani May 21 at 3:37

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Browse other questions tagged or ask your own question.