VMD-L Mailing List

From: Amira Yu (amirayuyue_at_gmail.com)
Date: Wed Jun 03 2015 - 17:39:49 CDT

Hi all,
  I am using VMD IR Spectra plugin on a small
ligand [1,1'-Biphenyl]-2,2'-diol (C12 H10 O2) 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