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

[Xavier Periole]

On Tue, 6 Jan 2009 18:46:39 +0800
  Dechang Li <li.dc06 at gmail.com> 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.
> 
> 	 Thank you for your reply! It was helpful. It was said that the index
> file only need 2 atoms, i.e. index of N and H. However, for the residue 
> PRO, how to define the vector NH? 
There is typically no signal for the residue Pro.
> 
> 
>>>>>>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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-----------------------------------------------------
XAvier Periole - PhD

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