Subject: Vibrational Simulation from Molecular Dynamic Data.

From: [email-masked] (David A. Tilbrook)
Date: Tue, 23 Jan 1996 20:42:50 +0000

Dear CCL List,

I have a problem with some data I am trying to analyse. I have carried out
molecular dynamics calculations for some straight chain aliphatic compounds
using the CFF93 force field. I can calculate the velocity auto-correlation
function and from this I can work out the power spectrum by using a fast
fourier transform.

I presume that this spectrum includes ALL modes corresponding to correlated
motion, ie. that BOTH Raman and normal IR vibrations are predicted.

Now I need to find a method to identify the IR active and Raman active modes.

As I understand it IR active modes correspond to vibrational transitions
which give rise to a change in dipole moment.

Now the dipole moment of a molecule can be calculated by its change in
charge distribution multiplied by the change in internal coordinates. Correct?

If so, does this mean that if I measure the on charge each atom using
Q-equilibration and multiply this by the velocity for each atom for each
frame of the dynamics trajectory that I will obtain a 'scaled' trajectory
file which when processed by the velocity autocorrelation function and
fourier transform will yield a scaled spectrum in the frequency domain which
gives an indication of modes which result in a change in dipole moment?

The charge could be used a a scalar as I would consider that the change in
charge would act directly along the axis of atoms velocity.

I am aware that errors in charge assignment could give some faults in thsi
analysis but would it work in theory at least?

I am plodding my way through the mathematics for a simple system presently
and would welcome any comments or findings of other workers.

I look forward to any comments you can make,

Regards,

David Tilbrook  ([email-masked])