[gmx-users] Re: gmx-users Digest, Vol 74, Issue 183

[Gerrit Groenhof]

I suggest you talk to the person(s) who did that experiment first, and find out what they measured and how.

If it is IR bands you're interested in, and depending on the system you can extract the complete IR spectrum by Fourier transformation of the time-dependent dipolemoment.


Gerrit


> 
> Date: Wed, 30 Jun 2010 12:57:22 +0200
> From: Baofu Qiao <qiaobf at gmail.com>
> Subject: Re: [gmx-users] question about Gromacs and Spectroscopy
> To: jalemkul at vt.edu, Discussion list for GROMACS users
> 	<gmx-users at gromacs.org>
> Message-ID: <4C2B2312.5050202 at gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
> 
> Hi Justin,
> 
> Thanks for your reply! And sorry for the vague question due to my little
> knowledge on the spectroscopy.
> 
> What I want to reproduce is wavenumber of C-H vibrations in alkyl
> chains. In NMR experiments, such wavenumber is measured to be 2000-3000
> cm-1, namely in the middle region of infra red. I wonder whether I can
> reproduce it or not?
> 
> I hope this is bit of clearer! Thanks a lot!
> 
> regards,
> Baofu Qiao
> 
> 
> Justin A. Lemkul wrote:
>> 
>> Baofu Qiao wrote:
>>> Hi all,
>>> 
>>> I want to reproduce some experimental data on Spectroscopy using
>>> Gromacs. I want to know is it possible? If yes, how to do that? Is there
>>> any tutorial related to that?
>>> 
>>> Any help is appreciate!
>>> 
>> 
>> Your question is too vague to get much useful advice.  The term
>> "spectroscopy" can refer to a large number of techniques.  I am
>> unaware of any tutorial related to any spectroscopic technique,
>> however, but you might get some useful advice if you ask a more
>> specific question (i.e., what you're actually trying to do).
>> 
>> -Justin
>> 
>>> regards,
>>> Baofu Qiao
>> 
> 
> 
> 
> ------------------------------
> 
> Message: 8
> Date: Wed, 30 Jun 2010 14:27:10 +0330
> From: shahab shariati <shahab.shariati at gmail.com>
> Subject: [gmx-users] g_rama / mult
> To: gmx-users at gromacs.org
> Message-ID:
> 	<AANLkTimj8-nnlXxA5jW_EgivNRrlWZmGeWKWOvVMeB4B at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
> 
> Hi all
> 
> I used  [ g_rama -f *.xtc -s *.tpr -o rama.xvg ] command for analysis of
> protein. gromacs give me rama.xvg as output but during calculation :
> 
> Found 68 phi-psi combinations
> Dihedral around 9,11 not found in topology. Using mult=3
> Dihedral around 11,18 not found in topology. Using mult=3
> Dihedral around 20,22 not found in topology. Using mult=3
> Dihedral around 22,29 not found in topology. Using mult=3
> Dihedral around 33,36 not found in topology. Using mult=3
> Dihedral around 40,47 not found in topology. Using mult=3
> Dihedral around 51,58 not found in topology. Using mult=3
> Dihedral around 62,65 not found in topology. Using mult=3
> Dihedral around 301,303 not found in topology. Using mult=3
> Dihedral around 303,314 not found in topology. Using mult=3
> Dihedral around 318,336 not found in topology. Using mult=3
> Dihedral around 340,358 not found in topology. Using mult=3
> Dihedral around 360,362 not found in topology. Using mult=3
> Dihedral around 362,378 not found in topology. Using mult=3
> Dihedral around 382,393 not found in topology. Using mult=3
> Dihedral around 397,407 not found in topology. Using mult=3
> Dihedral around 411,424 not found in topology. Using mult=3
> Dihedral around 428,446 not found in topology. Using mult=3
> Dihedral around 450,467 not found in topology. Using mult=3
> Dihedral around 471,486 not found in topology. Using mult=3
> Dihedral around 490,497 not found in topology. Using mult=3
> Dihedral around 509,511 not found in topology. Using mult=3
> Dihedral around 523,525 not found in topology. Using mult=3
> Dihedral around 529,540 not found in topology. Using mult=3
> Dihedral around 544,564 not found in topology. Using mult=3
> Dihedral around 568,586 not found in topology. Using mult=3
> Dihedral around 590,610 not found in topology. Using mult=3
> Dihedral around 614,629 not found in topology. Using mult=3
> Dihedral around 633,639 not found in topology. Using mult=3
> Dihedral around 643,661 not found in topology. Using mult=3
> Dihedral around 665,678 not found in topology. Using mult=3
> Dihedral around 682,697 not found in topology. Using mult=3
> Dihedral around 701,714 not found in topology. Using mult=3
> Dihedral around 718,733 not found in topology. Using mult=3
> Dihedral around 737,744 not found in topology. Using mult=3
> Dihedral around 748,759 not found in topology. Using mult=3
> Dihedral around 763,783 not found in topology. Using mult=3
> Dihedral around 787,800 not found in topology. Using mult=3
> Dihedral around 804,816 not found in topology. Using mult=3
> Dihedral around 820,838 not found in topology. Using mult=3
> Dihedral around 842,852 not found in topology. Using mult=3
> Dihedral around 856,876 not found in topology. Using mult=3
> Dihedral around 880,896 not found in topology. Using mult=3
> Dihedral around 900,913 not found in topology. Using mult=3
> Dihedral around 917,927 not found in topology. Using mult=3
> Dihedral around 931,951 not found in topology. Using mult=3
> Dihedral around 955,975 not found in topology. Using mult=3
> Dihedral around 979,985 not found in topology. Using mult=3
> Dihedral around 989,1007 not found in topology. Using mult=3
> Dihedral around 1011,1031 not found in topology. Using mult=3
> Dihedral around 1035,1055 not found in topology. Using mult=3
> Dihedral around 1059,1079 not found in topology. Using mult=3
> Dihedral around 1083,1090 not found in topology. Using mult=3
> Dihedral around 1094,1097 not found in topology. Using mult=3
> Dihedral around 1109,1111 not found in topology. Using mult=3
> Dihedral around 1115,1122 not found in topology. Using mult=3
> Dihedral around 1126,1133 not found in topology. Using mult=3
> 
> is this rama.xvg file true and intact?
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> End of gmx-users Digest, Vol 74, Issue 183
> ******************************************

--
Gerrit Groenhof
MPI biophysical chemistry
Goettingen
Germany
http://wwwuser.gwdg.de/~ggroenh/