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From: Arvid Soederhaell <arvid_at_fmp-berlin.de>

Date: Fri 12 Apr 2002 14:55:33 +0200 (MEDT)

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

Received on Fri Apr 12 2002 - 05:55:33 PDT

Date: Fri 12 Apr 2002 14:55:33 +0200 (MEDT)

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

Received on Fri Apr 12 2002 - 05:55:33 PDT

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