Dear amber users ,
I want to calculate generalized order parameters of each amino acid residues (N-H vector) by molecular dynamics simulation.
And compare it to order parameters derived from NMR experiment .
It seems that ptraj support two methods suitable for calculating order parameters from dynamic trajectory .
One method calculate it directly from Legendre polynomial .
Ane the other one calculate it using iRED technique .
>From the amber9 manual , I know some key words related to such analysis. (VECTOR , MATRIX ,ANALYZE MATRIX)
However , i don't know how to carry out such analysis exactly.
Could you please give me a copy of input file used for analyzing order parameters ?
Thank you very much for your kindly help.
2007-10-28
cgji
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Received on Wed Oct 31 2007 - 06:07:08 PDT
