[gmx-users] calculation of the order parameter S2

Xavier Periole X.Periole at rug.nl
Sun Jan 4 14:52:47 CET 2009

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
>>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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