AMBER Archive (2006)

Subject: AMBER: Ptraj: diffusion rate

From: Austin B. Yongye (
Date: Tue Nov 21 2006 - 15:03:52 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 from the diffusion analysis increase to some point, and then
decrease again. I don't know if this is what I should expect.
I have attached the graphs I get from the ptraj analysis.

Here are my inputs:
1. Diffusion:
trajin md.crd
diffusion :1-3 0.5 average malt_diff

Any help will be greatly appreciated.

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