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-boun...@gromacs.org 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: > > 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. > 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: http://pubs.acs.org/doi/abs/10.1021/jp902131b http://www3.interscience.wiley.com/journal/114209721/abstract -Justin > > > Thank you, > > Sarah > -- ======================================== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- 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 -- 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