[gmx-users] Re: Re: calculation of the order parameter S2 (Xavier Periole)

Dechang Li li.dc06 at gmail.com
Mon Jan 5 12:15:57 CET 2009

>Message: 4
>Date: Sun, 04 Jan 2009 14:52:47 +0100
>From: "Xavier Periole" <X.Periole at rug.nl>
>Subject: Re: [gmx-users] calculation of the order parameter S2
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Message-ID: <web-103138727 at mail3.rug.nl>
>Content-Type: text/plain;charset=utf-8;format="flowed"
>On Sun, 04 Jan 2009 13:38:33 +1100
>  Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
>> Dechang Li wrote:
>>> Dear all, 
>>>     I want to use g_rotacf to calculate the order parameter(S2, N-H bond in 
>>>main chian).
>>> The tool g_rotacf needs an index.ndx file that contains two vectors. 

>g_rotacf wants the index number of two atoms to calculate the order
>parameter of an NH vector. You should give the index number of the atoms
>N and H and use the option -d. Note that you have to take care of the
>overall rotation of the molecule in the calculation. Either you remove
>it before the calculation or you include it in the fit of the correlation

   I read the manual that the index file should contain 3 atoms, i.e. (i, j, k).
Is that mean I should write the index file like this:

[ group1 ]
1 3 4
[ group2 ]
5 8 9

   where 1 for atom Ca, 3 for atom N, and 4 for atom H, in a peptide?


>>>How can I make the 
>>> index.ndx file? Can I use the tool make_ndx to do this? Or I need to write 
>>>the file manually?
>> See http://wiki.gromacs.org/index.php/Index_File. I think you just want
>> to write a file by hand.
>> Mark
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>XAvier Periole - PhD
>- Molecular Dynamics Group -
>Computation and NMR
>University of Groningen
>The Netherlands
>gmx-users mailing list
>gmx-users at gromacs.org
>Please search the archive at http://www.gromacs.org/search before posting!
>End of gmx-users Digest, Vol 57, Issue 4

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