VMD-L Mailing List

From: Daniel Möller (daniel.moeller3_at_uni-greifswald.de)
Date: Thu Jun 04 2015 - 13:51:07 CDT

Hi,

 

no, I’ve no idea why. But please use “response to all”, so that your question goes to the mailing list too.

 

 

Sincerely

 

Daniel Möller

 

 

 

Von: Amira Yu [mailto:amirayuyue_at_gmail.com]
Gesendet: Donnerstag, 4. Juni 2015 20:15
An: Daniel Möller
Betreff: Re: vmd-l: IR Spectroscopy plugin questions

 

Hi Daniel,

  I have another question, when I turned off the rigid bond (rigidBonds none) I can successfully get a higher wave number signal, but I kept getting a very high peak at 1750 1/cm, whereas the experimental wavenumber should around 1500 1/cm for the benzene rings. My structure is two benzene rings connect to one hydroxyl group. Do you know any potential reasons causing that problem?

  Thank you again.

Best regards,

Yue

 

2015-06-04 14:04 GMT-04:00 Amira Yu <amirayuyue_at_gmail.com>:

Hi Daniel,

  Thank you so much for your suggestion. I fixed it and now it works.

Sincerely,

Yue

 

2015-06-04 13:57 GMT-04:00 Daniel Möller <daniel.moeller3_at_uni-greifswald.de>:

Hi,

 

rigid bonds could be your problem, cause it fix the hydrogen bond.

 

 

Sincerely

 

Daniel Möller

 

 

 

Von: Amira Yu [mailto:amirayuyue_at_gmail.com]
Gesendet: Donnerstag, 4. Juni 2015 16:29
An: Daniel Möller

Betreff: Re: vmd-l: IR Spectroscopy plugin questions

 

Hi Daniel,

  I used rigid bond in NAMD and SHAKE in CHARMM, and I also changed the output .dcd frequency to 1 but still can't see anything after 1000 (1/cm) wavenumber. I even set my time step to 0.1fs in NAMD but still doesn't help.

  I used the solvated system to run CHARMM first to minimize my system and heat to room temp. for 15ps followed by a 100ps NPT equilibration, then I put this minimized system to NAMD to run a 5ps simulation. I used the trajectory from NAMD to get the IR. I don't know what is wrong with my set up that I cannot get any signal in high wave number region.

  Thank you in advance.

Sincerely,

Yue

 

2015-06-04 6:35 GMT-04:00 Daniel Möller <daniel.moeller3_at_uni-greifswald.de>:

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

  

--
------------------------
Dipl. Biochem. Daniel Möller
 
Biophysical Chemistry
Institut of Biochemistry
Unversity of Greifswald
Felix-Hausdorff-Strasse 4
17489 Greifswald - Germany
 
Tel +49 3834 86 4406 <tel:%2B49%203834%2086%204406> 
 
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
 
 
 
-- 
Chemical Engineering
YU Yue
859-536-6507
 
-- 
Chemical Engineering
YU Yue
859-536-6507
 
-- 
Chemical Engineering
YU Yue
859-536-6507
 
-- 
Chemical Engineering
YU Yue
859-536-6507