[gmx-users] By using the Gromacs to simulate Raman spectrum

[Alex]

There's sort of no point in doing that, or, rather doing the simulations.
Given the type of interactions most of biophysics forcefields have
(harmonic springs), you can in fact calculate everything without any
simulations. That is, if you never use constrained bonds. If you do use
constrained bonds, your frequencies will approach infinity, because the
resulting bond stiffness is very high. A relatively decent way of doing
vibrational analysis for organics is with DFT, e.g. with Gaussian, which
has provisions for determining the frequencies. You probably will not be
able to actually plot Raman spectra, but instead you could simulate the
peaks observed in Raman spectra.

Alex

On Tue, Jun 27, 2017 at 12:36 PM, lu lu <lulu9091 at gmail.com> wrote:

> Greeting,
>
>   Hello, I am a new beginner for Gromacs. Our group is trying to simulate
> Raman spectrum for a variety of small organic molecules, like amino acid
> and ribonucleic acid.
>
>  I was planning to use both GAMESS and Gromacs to simulate the Raman
> Spectrum for tyrosine. My plan was simulated the single tyrosine molecule
> by GAMESS and use the Gromacs to simulate clustered tyrosine behavior and
> extract the Raman spectrum from it. However, after I did some research
> online, I found out that, almost no one uses Gromacs to do the vibrational
> spectrum. It seems like Gromacs is mainly used for simulating the
> interaction dynamics between small molecules like nanoparticles interacting
> with lipid membrane.
>
>  So, my question is, it is possible to use Gromacs to do the simulation for
> Raman spectrum? If so, would anyone show a direction for how to get it?
>
>  Thank you for your guys helping,
>
>  Best Regards,
>  Lu
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