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

Dechang Li li.dc06 at gmail.com
Tue Jan 6 11:46:39 CET 2009

>>>> 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, 
>> 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? 

>>>>>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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