[AMBER] analysising trajectory

From: Homa Azizian <homa.azizian.anu.edu.au>
Date: Thu, 08 Jul 2010 12:05:30 +1000

Hi all,
I have done 50 ns simulation, and I want to analysis cross-correlation of C-alpha .
in 3 different simulation time: 1-10 ns, 11-30 ns, 31-50 ns. I use 2 different strategy to filter internal rotation and translation. 1-first strucure and average structure. in both of these to strategy the rmsf of 11-30 ns simulation is bigger than the others (1-10 ns, 31-50 ns). I mean that the rmsf of the first 9 ns is low then from 11-30 ns it increases and then from 31-50 ns it is again decreased.
also about the 2d-plot of cross correlation, the 11-30 ns has pronounced coorelated and anti-correlated region which is disapeard in the last 20 ns (31-50).
I want to know that is it sence, becase the equilibration state is reached in the first 4 ns, and I expect that the result of 11-30ns would be the same as 31-50 ns.
I realy appreciated any comments
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Received on Wed Jul 07 2010 - 19:30:02 PDT
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