

AMBER Archive (2008)Subject: AMBER: Correlation functions from iRED analysis From: Samuel Genheden (a03samge) (a03samge_at_student.his.se)Date: Thu Jun 19 2008  05:22:53 CDT
Hello, Amber users
I'm studying a protein using MD and would like to calculate correlation functions with the iRED method in order to compare order parameters from NMR. My protein is 138 residues long and contains 10 prolines, and therefore I have 128 NH vectors. I'm using Amber10. My input file looks like this:
trajin ../mdcrd5.gz
(I've have also tried to break it up in two ptraj scripts, since the manual is a little bit vague if this is neccessary.) The problem is that all the correlation functions calculated, v2.out, v3.out, .. v138.out is the same, i.e. all the output files contains the same numbers. What am I doing wrong? I can hardly believe that all the correlation functions should be identical.
And when I'm at writing  what is the best way to obtain the order parameters from the correlation functions?
Best regards, Samuel

 
