[gmx-users] Order parameter for unsaturated lipid chain in UA model

Sarah Witzke sawit02 at student.sdu.dk
Thu Feb 25 13:58:58 CET 2010

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:


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,


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