VMD-L Mailing List

From: Daniel Möller (daniel.moeller3_at_uni-greifswald.de)
Date: Thu Jun 04 2015 - 05:35:50 CDT

Hi,

 

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

 

 

Sincerely

 

Daniel Möller

  

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Dipl. Biochem. Daniel Möller
 
Biophysical Chemistry
Institut of Biochemistry
Unversity of Greifswald
Felix-Hausdorff-Strasse 4
17489 Greifswald - Germany
 
Tel +49 3834 86 4406
 
http://www.mnf.uni-greifswald.de/institute/institut-fuer-biochemie/biophysikalische-chemie.html
 
 
Von: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] Im Auftrag von Amira Yu
Gesendet: Donnerstag, 4. Juni 2015 03:43
An: vmd-l_at_ks.uiuc.edu
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.
Sincerely.
Yue
 
2015-06-03 19:33 GMT-04:00 Josh Vermaas <vermaas2_at_illinois.edu>:
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 (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
 
 
 
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Chemical Engineering
YU Yue
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