VMD-L Mailing List
From: Daniel Möller (daniel.moeller3_at_uni-greifswald.de)
Date: Thu Jun 04 2015 - 12:57:00 CDT
rigid bonds could be your problem, cause it fix the hydrogen bond.
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
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.
2015-06-04 6:35 GMT-04:00 Daniel Möller <daniel.moeller3_at_uni-greifswald.de>:
to you use rigid bonds in NAMD? Or other parameters to make your simulation go faster at the costs of accuracy?
-- ------------------------ 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