AMBER Archive (2002)

Subject: order parameters?

From: Arvid Soederhaell (arvid_at_fmp-berlin.de)
Date: Fri Apr 12 2002 - 07:55:33 CDT

Dear All

I am trying to calculate the order parameters from a membrane simulation.
The thing that has to be done is:

1. Define the membrane normal.

2. Use the bonds C-H in the lipid tails to define a vector. In my case
(64 DPPC lipids) there is 64*14*2*2=3584 such vectors (Number of
lipids*number of CH2 groups in each lipid tail*2 tails per lipid*2 C-H
bonds in each CH2 group).

3. Calculate the angle between the normal defined in 1. and the vectors
defined in 2.

4. Average over all lipids, distinguish between the separate CH2 groups.
That is, i want the average angle for C1, C2, ... C14 in all lipids,
where C1, C2, etc. are the CH2 groups in the lipid tail.

5. The rest is quite simple mathematics...

My problem is that do not know how to do step 1-4 using the AMBER analysis
programs. With ptraj you can do point 2. using the vector command, but it
becomes very messy when using 3584 vector commands.

Best regards
   Arvid Soderhall

Arvid Soederhaell, PhD Phone:+49-30-94793-231
Forschungsinstitut fuer Molekulare Pharmakologie
Robert-Roessle-Strasse 10 Fax::+49-30-94793-169
131 25 Berlin