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correl.doc provides the syntax for its traj subcommand; see also dynamc.doc.

We do not know how you specified only one frame, because you have not shown us the traj command you used. Does your trajectory contain more than one frame?


Lennart Nilsson
Karolinska Institutet
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I should note that the script computes averages for a given C-H vector over all lipids and time points, but does not average the two values for the two vectors on the same C atom; you would need to that. They are not averaged because the equivalence of the two values is an indication of convergence; for a well converged analysis interval, the values should agree fairly closely.


Rick Venable
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Hi, can we use above code to calculate the order parameters of PIP2? It looks like it also has the specified carbon atoms.

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