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#34480 - 10/07/14 11:49 AM Re: lipid C-D order parameters using CORREL [Re: rmv]
lennart Online   content

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Registered: 09/25/03
Posts: 4741
Loc: ~ 59N, 15E
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?
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Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

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#34481 - 10/07/14 02:20 PM Re: lipid C-D order parameters using CORREL [Re: rmv]
rmv Online   content

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Registered: 09/17/03
Posts: 8373
Loc: 39 03 48 N, 77 06 54 W
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.
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Rick Venable
computational chemist


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