AMBER Archive (2001)

Subject: computing order parameters from an MD trajectory

From: Jake Isaacs (rjisaa0_at_uky.edu)
Date: Mon Aug 27 2001 - 09:45:58 CDT

The documentation for ptraj states that order parameters can be calculated
from an MD trajectory, but doesn't go into details. I would like to compare
my MD results with NMR based order parameters. I have removed solvent from
my trajectory, imaged it, and superimposed all frames to remove rotation and
translation. How can I now compute the order parameters for specific C-H
vectors?

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