order parameter, lipid segments as vectors

From: Raul Araya (arayasecchi_at_gmail.com)
Date: Tue Oct 27 2009 - 08:48:32 CDT

Dear NAMD users:

Im running simulations of Dotriacontane films over a SiO2 waffer, and
Im interested in measure the P2 (legendre polinomial) order parameter
in wich one measures the angle between the molecule (or a segment of
the molecule) and the Z axis of the system and with that information
one can calculate the order parameter P2 to describe the ordering of
lipid molecule over the SiO2 waffer (parallel or perpendicular). I
want to make a tcl script that allowme to measure the angle between
segments of the dotriacontane molecule (segments of 8 carbon atoms for
example) and the Z axis. What I want to know is how can I define the
dotriacontane segments as a vectors so I can measure the angle between
each vector and the Z axis. Please If any one can helpme construct my
tcl script or already have a similar script please help me...

Thanks very much.

Ral Araya Secchi
B.Sc Molecular Biotechnology.
Molecular Biotechnology Engineer.
Centre for Bioinformatics CBUC,
Faculty of Biological Sciences, P. Universidad Catolica de Chile
Portugal # 49 ZIP 6513492 Santiago Chile Phone: + 56 2 6862269;

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