CHARMM Development Project Forums CHARMM Community Script Archive lipid C-D order parameters using CORREL

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Re: lipid C-D order parameters using CORREL rmv #34480 10/07/14 03:49 PM
Joined: Sep 2003 Posts: 4,881 Likes: 12 ~ 59N, 15E lennart Forum Member
lennart Forum Member Joined: Sep 2003 Posts: 4,881 Likes: 12 ~ 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? Lennart Nilsson Karolinska Institutet Stockholm, Sweden

Re: lipid C-D order parameters using CORREL rmv #34481 10/07/14 06:20 PM
Joined: Sep 2003 Posts: 8,650 Likes: 26 39 59 56 N, 77 06 07 W rmv OP Forum Member
OP rmv Forum Member Joined: Sep 2003 Posts: 8,650 Likes: 26 39 59 56 N, 77 06 07 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. Rick Venable computational chemist

Re: lipid C-D order parameters using CORREL rmv #37959 07/05/20 07:14 PM
Joined: Aug 2009 Posts: 139 L lqz Forum Member
lqz Forum Member L Joined: Aug 2009 Posts: 139	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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