From: Daniel Möller (
Date: Thu Jun 04 2015 - 05:35:50 CDT



to you use rigid bonds in NAMD? Or other parameters to make your simulation go faster at the costs of accuracy?





Daniel Möller


Dipl. Biochem. Daniel Möller
Biophysical Chemistry
Institut of Biochemistry
Unversity of Greifswald
Felix-Hausdorff-Strasse 4
17489 Greifswald - Germany
Tel +49 3834 86 4406
Von: [] Im Auftrag von Amira Yu
Gesendet: Donnerstag, 4. Juni 2015 03:43
Betreff: Re: vmd-l: IR Spectroscopy plugin questions
Hi Josh,
  Thank you so much for your suggestions, and I have tried to change my time step even to 0.1 fs and changed the output .dcd save frequency to 1 but still see nothing in the high (>1000 1/cm) wave number region. Do you think anything else would cause this kind of problem?
  Thank you again.
2015-06-03 19:33 GMT-04:00 Josh Vermaas <>:
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.
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 (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. 
Chemical Engineering
YU Yue