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
=========================================
Dechang Li, Ph.D Candidate
Department of Engineering Mechanics
Tsinghua University
Beijing 100084
P.R. China
Tel: +86-10-62773574(O)
Email: lid...@mails.tsinghua.edu.cn
=========================================
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