[gmx-users] question about Gromacs and Spectroscopy
mark.abraham at anu.edu.au
Wed Jun 30 16:17:46 CEST 2010
----- Original Message -----
From: Baofu Qiao <qiaobf at gmail.com>
Date: Wednesday, June 30, 2010 20:57
Subject: Re: [gmx-users] question about Gromacs and Spectroscopy
To: jalemkul at vt.edu, Discussion list for GROMACS users <gmx-users at gromacs.org>
> Hi Justin,
> Thanks for your reply! And sorry for the vague question due to
> my little
> knowledge on the spectroscopy.
> What I want to reproduce is wavenumber of C-H vibrations in alkyl
> chains. In NMR experiments, such wavenumber is measured to be
> cm-1, namely in the middle region of infra red. I wonder whether
> I can
> reproduce it or not?
So you'll need to calculate accurate force constants of molecular vibrations of meaningful conformations.
MD might be good for getting to sample a useful set of conformations, but QM on the resulting conformations will give you better estimates of force constants. It sounds like you need to spend some time reading up on this stuff.
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