From: Raman Preet Singh (ramanpreetsingh_at_hotmail.com)
Date: Fri Feb 12 2021 - 05:14:36 CST
Thanks Andre for the info. This was indeed very useful.
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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
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.
On Fri, Feb 12, 2021 at 7:41 AM Raman Preet Singh <ramanpreetsingh_at_hotmail.com<mailto:ramanpreetsingh_at_hotmail.com>> wrote:
I posted this earlier but received no directions. Reposting the same in case someone who might help me missed it.
Thanks in advance.
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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<mailto:namd-l_at_ks.uiuc.edu>>
Subject: Infrared spectrum prediction
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.
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