Dear gmx users,
I am sorry to ask this question again, but reading in the email achieve did not enlighten me. I found this email which describes my problem, but unfortunately it has no replies: http://lists.gromacs.org/pipermail/gmx-users/2008-July/034950.html Also there are these two recently emails: http://lists.gromacs.org/pipermail/gmx-users/2010-January/047767.html <http://lists.gromacs.org/pipermail/gmx-users/2010-January/047767.html> , but I am still in doubt. So my question is regarding the unsaturated lipid chain of POPC. I would like to calculate the order parameters for my united atoms so I make first an index file with the tail atoms from the carbonyl-C to the methyl-C and then I run g_order -od. Then I make a new index file with the two atoms of the double bond and the atom before and after the double bond (four atoms in total) running g_order -unsat -od I then take the two values from the last g_order run and replace them with the order parameters for the double bond calculated without -unsat. When looking at the graph and comparing to the literature this graph it looks wrong: First there is a small dip in the order for the atom before the double bond, then it goes a bit up for the first double bonded C, and then for the next double bonded C and the atom after that the order is quite low. I know this description is not good, but it was just to explain, that the graph is not as expected. I would very much appreciated if anyone could tell me, where I go wrong. Thank you, Sarah -- gmx-users mailing list gmx-users@gromacs.org http://lists.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
