AMBER Archive (2006)

Subject: AMBER: Ptraj: correlation time

From: Austin B. Yongye (
Date: Tue Nov 21 2006 - 15:05:52 CST

Dear amber users,
I am using ptraj to determine the diffusion rate and correlation time of a
trisaccharide, from two 10-ns MD simulations. The only difference between
the simulations, is the retention of translational and rotational COM
motions in one (nscm=0).
The graphs I get from the ptraj correlation analysis, do not decay smoothly.
I have attached the graphs I get from the ptraj analysis.

Here is my input:
1. Correlation:
trajin md.crd
correlation cor2 :3_at_C1 :3_at_H1 1 20000 20000 out res3C1_res3H1_corr.out go

Any help will be greatly appreciated. I would also like to know what the
three columns stand for.

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