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

[Dechang Li]

>>>> 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? 


>>>>>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
>>>> _______________________________________________
>>>> gmx-users mailing list    gmx-users at gromacs.org
>>>> http://www.gromacs.org/mailman/listinfo/gmx-users
>>>> Please search the archive at http://www.gromacs.org/search before posting!
>>>> Please don't post (un)subscribe requests to the list. Use the 
>>>> www interface or send it to gmx-users-request at gromacs.org.
>>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>>
>>>-----------------------------------------------------
>>>XAvier Periole - PhD
>>>
>>>- Molecular Dynamics Group -
>>>Computation and NMR
>>>University of Groningen
>>>The Netherlands
>>>-----------------------------------------------------