[gmx-users] index file for DPPC

[Kukol, Andreas]

Dear Caty,

You have to make an index file containing groups for each type of atom in one of your tails (e.g. the sn1-chain), that means for dppc you end up with 15 groups: C11, C12, C13, ...
Each group will have 100 elements.

For the sn2-chain you need to make a separate index file.

Andreas

>>>>>>>
From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of koukoulitsa at eie.gr
Sent: 22 January 2009 11:15
To: gmx-users at gromacs.org
Subject: [gmx-users] index file for DPPC

Dear all gmx_users,

I want to calculate the order parameter after the incorporation of a molecule of DHA in the DPPC Bilayer (100 DPPC lipids).

I have read in the manual that the program can gives an idea of the ordering of a molecule from head to tail and I have read that I have to construct an index file, but I don't know how I can group all the CH2 segments that are necessery for this calculation.

I will appreciate your help,

thanks in advance!

Caty.



Dr. Koukoulitsa Catherine
Laboratory of Molecular Analysis
Institute of Organic & Phamaceutical Chemistry
Hellenic National Research Foundation
Vas. Konstantinou 48
11635, Athens
Greece

Tel: +30-210-7273869-71
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