[gmx-users] generalized order parameters S2

[Dechang Li]

Dear all, 

    I have run a 100ns simulation of protein. I want to calculate the 
generalized order parameters S2 for N-H. It was said that to calculate
 S2, the overall motion should be subtracted first. How can I subtract
the overall motion? Can I use the command 'trjconv' to fit the protein 
to a reference strucutre firstly, and then calculate S2 using command 
'g_rotacf'? If YES, what the reference structure is? The average
structure in the trajectory? 




Best regards,
2009-3-3



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Dechang Li, Ph.D Candidate
Department of Engineering Mechanics
Tsinghua University
Beijing 100084
P.R. China 

Tel:   +86-10-62773574(O) 
Email: lidc02 at mails.tsinghua.edu.cn
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