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Re: lipid C-D order parameters using CORREL
rmv #34480 10/07/14 03:49 PM
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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
Stockholm, Sweden
Re: lipid C-D order parameters using CORREL
rmv #34481 10/07/14 06:20 PM
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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
computational chemist

Re: lipid C-D order parameters using CORREL
rmv #37959 07/05/20 07:14 PM
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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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