>Message: 4
>Date: Sun, 04 Jan 2009 14:52:47 +0100
>From: "Xavier Periole" <[email protected]>
>Subject: Re: [gmx-users] calculation of the order parameter S2
>To: Discussion list for GROMACS users <[email protected]>
>Message-ID: <[email protected]>
>Content-Type: text/plain;charset=utf-8;format="flowed"
>
>On Sun, 04 Jan 2009 13:38:33 +1100
> Mark Abraham <[email protected]> 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?
>>>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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