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-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of koukouli...@eie.gr Sent: 22 January 2009 11:15 To: gmx-users@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 Fax: +30-210-7273872 Web: www.eie.gr _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
