AMBER Archive (2009)

Subject: Re: [AMBER] Low frequency Raman spectra

From: case (case_at_biomaps.rutgers.edu)
Date: Sat Nov 07 2009 - 09:02:02 CST

On Sat, Nov 07, 2009, babak minoofar wrote:

> I would likeĀ to calculate low frequency Raman
> spectra of organic solvent such as Formamide for this I have to do
> Fourier transformation of velocity correlations of solvent molecules in
> order to get comparable data with low frequency Raman spectra. Can
> anybody help me with this task? Is anybody is using any script which can
> read AMBER trajectory and to do such calculations

Yes, and mostly, no. Amber *does* have the ability to compute vibrational
spectra of liquids, but this is a very advanced subject, and not yet a matter
of just running a script.

To see what is involved, you might look at these papers:

F. Paesani, W. Zhang, D.A. Case, T.E. Cheatham III, and G.A. Voth. An
accurate and simple quantum model for liquid water. J. Chem. Phys. 125,
184507 (2006).

J. Liu, W.H. Miller, F. Paesani, W. Zhang, and D.A. Case. Quantum
dynamical effects in liquid water: A semiclassical study on the diffusion
and the infrared absorption spectrum. J. Chem. Phys. 131, 164509 (2009)

Dr. Liu is in the process of creating a tutorial on how to carry out such
calculations, but it will not be ready for several months. We also do not
have any built-in procedure to handle Raman (as opposed to infrared) spectra.

If you think that just knowing the purely classical velocity-velocity
correlations would be enough, you could save velocities while running the
trajectory (the ntwv variable), then write scripts to analyze these.

...good luck....dac

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