SV: [gmx-users] Order parameter for unsaturated lipid chain in UAmodel

Sarah Witzke sawit02 at
Thu Feb 25 14:51:27 CET 2010

Thank you for your quick respons! It is not so much the drop, but more the position and the prescens of a small drop, then a little rise and then the big drop. I have pasted the file in below.
Do you think my method of replacing the order parameters for the double bonded atoms is ok?
****************Order parameters sn-2 chain POPC*********
           1       0.176177
           2        0.18184
           3       0.182874
           4       0.180724
           5       0.167932
           6       0.162731
           7       0.107512
           8       0.139351
           9      0.0311607
          10      0.0519802
          11       0.095191
          12      0.0884555
          13      0.0930531
          14      0.0787042
          15      0.0732823
          16      0.0541174

Thank you, Sarah


Fra: gmx-users-bounces at på vegne af Justin A. Lemkul
Sendt: to 25-02-2010 14:42
Til: Discussion list for GROMACS users
Emne: Re: [gmx-users] Order parameter for unsaturated lipid chain in UAmodel

Sarah Witzke wrote:
> 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: <> , 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.

I don't see why a drop in the order parameter is unexpected.  I see it all the
time in published papers of unsaturated lipids, for example:


> Thank you,
> Sarah


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at] | (540) 231-9080

gmx-users mailing list    gmx-users at
Please search the archive at before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at
Can't post? Read

More information about the gromacs.org_gmx-users mailing list