VMD-L Mailing List

From: Richard Swenson (swenson_at_hec.utah.edu)
Date: Fri Jun 01 2007 - 09:21:07 CDT

Dear all,

I neglected to attach my order parameter in my last post. I am looking
for a better script, or suggestions for improvement of my script, that
will compute the order parameters for a non-planar bilayer for a large
system (1440 lipids) in less than the month that this one will take.

This script is broken into five parts:

1. The first process accepts an index of an atom on a given lipid, a
radius, and a frame number. The process the returns a vector in the
form of a list that is the normal of the plane that best fits the
positions of all the phosphorus atoms on the same leaflet as the point
atom and within the radius.

2. The second process is dead code that computes order parameters with
the assumption that the bilayer normal is in the z direction. When
used, this code took about a day to compute the order parameters of 1440
lipids over 300+ frames.

3. This third process uses carbons and the computed bilayer normal to
compute order parameters.

4. This fourth process uses either the second or third process to loop
over the specified lipids, carbons and chains.

5. This chunk of code removes many unneeded residues in order to free
up memory and then specifies which lipids, carbons, and chains will be
analyzed.

Thanks for the feedback,
Richard