Re: Re: Infrared spectrum prediction

From: Andre Farias de Moura (moura_at_ufscar.br)
Date: Fri Feb 12 2021 - 07:35:43 CST

Dear Raman,

If your system is small enough, I would recommend ab initio MD to avoid the
harmonic approximation issues and also possible parameterization caveats.

Regards

Andre

On Fri, Feb 12, 2021 at 8:14 AM Raman Preet Singh <
ramanpreetsingh_at_hotmail.com> wrote:

> Thanks Andre for the info. This was indeed very useful.
>
> Regards,
> Raman
>
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> ------------------------------
> *From:* Andre Farias de Moura <moura_at_ufscar.br>
> *Sent:* Friday, February 12, 2021 4:29:00 PM
> *To:* namd-l_at_ks.uiuc.edu <namd-l_at_ks.uiuc.edu>; Raman Preet Singh <
> ramanpreetsingh_at_hotmail.com>
> *Subject:* Re: namd-l: Re: Infrared spectrum prediction
>
> Dear Raman,
>
> Although most people to date have relied on normal mode analysis to
> predict IR features, MD simulations can be used as well, with the advantage
> of sampling multiple energy minima (as compared to the single minimum in
> energy minimization protocols). It does not matter whether you have a large
> protein or small molecule in vacuum, procedures will be pretty much the
> same (maybe you might want to look at the TRAVIS program, which can handle
> MD simulations to extract IR).
>
> Please mind that you will still need normal mode analysis to assign the IR
> bands, since MD-based spectra yield only the convoluted bands.
>
> Regards
>
> Andre
>
> On Fri, Feb 12, 2021 at 7:41 AM Raman Preet Singh <
> ramanpreetsingh_at_hotmail.com> wrote:
>
> Dear All,
>
> I posted this earlier but received no directions. Reposting the same in
> case someone who might help me missed it.
>
> Thanks in advance.
>
> RPS
>
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>
> ------------------------------
> *From:* Raman Preet Singh
> *Sent:* Monday, January 18, 2021 11:51:23 PM
> *To:* NAMD list <namd-l_at_ks.uiuc.edu>
> *Subject:* Infrared spectrum prediction
>
> Dear All,
>
> I have come across some papers where MD has been used to predict IR
> spectrum of proteins. Is it possible to predict IR spectrum of small
> organic molecules from NAMD simulations? Can changes in IR spectra due to
> interactions between two molecules (H-bonding, pi-pi interactions, etc ) be
> also predicted? Any papers, tutorials, scripts, etc. would be highly
> appreciated.
>
> Thanks in advance.
>
> Regards,
> Raman
>
>
>

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