VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Wed Jun 03 2015 - 18:33:48 CDT

Hi Yue,

How often are you saving your trajectory? One of the usual hangups is
that in order to see features above ~1000 wavenumbers, you basically
need to save your trajectory incredibly frequently (every femtosecond is
what I seem to remember), which has to do with the fact that those
high-wavenumber modes (bond stretches to hydrogen) have periods on the
order of a few femtoseconds, and if you don't give the plugin data that
is at a similar resolution, you won't see anything.

-Josh

On 6/3/15 5:39 PM, Amira Yu wrote:
> Hi all,
> I am using VMD IR Spectra plugin on a small
> ligand [1,1'-Biphenyl]-2,2'-diol (C_12 H_10 O_2 ) in order to test the
> parameters. I have trajectory file (.dcd file) and the .psf file.
> However, the IR plot doesn't have any signal after 1000 (1/cm). The
> trajectory I am using is from NAMD simulation, the system put into
> NAMD was after minimization and equilibration using CHARMM (100ps
> equilibration). I use 5 ps trajectory from NAMD to get the IR
> spectroscopy. When I compared with the experimental IR plot which has
> an obvious peak around 3300 (1/cm), whereas I cannot see any signal
> after 1000 (1/cm) in my VMD IR plugin result, does anyone know what is
> the problem in my setup?
> Any suggestions will be appreciated.
> Sincerely,
> Yue
>