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

[Xavier Periole]

On Mon, 5 Jan 2009 19:15:57 +0800
  Dechang Li <li.dc06 at gmail.com> wrote:
> 
>>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
>>function.
> 
>   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?
This will not define a vector! To follow the movement of the NH vector
(made of two atoms! the N and the H) you need only two index numbers, the
one of the N and the one of the H. Then the option -d is needed for
g_rotacf to treat the corresponding vector.
> 	
> 
> 
> 
>>>>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
>>-----------------------------------------------------
>>
>>
>>------------------------------
>>
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>>End of gmx-users Digest, Vol 57, Issue 4
>>****************************************
> 
> 
> 
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-----------------------------------------------------
XAvier Periole - PhD

- Molecular Dynamics Group -
Computation and NMR
University of Groningen
The Netherlands
-----------------------------------------------------