SV: [gmx-users] Order parameter for unsaturated lipid chain in UAmodel
Sarah, I remember some changes to the double bond awhile back, perhaps you're using those? POPC (Berger/Tielman) is normally 'smoother' as Justin says. Maybe someone has a reference for the updates. Tim Sirk -- gmx-users mailing listgmx-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
SV: [gmx-users] Order parameter for unsaturated lipid chain in UAmodel
Sarah, I remember some changes to the double bond awhile back, perhaps you're using those? POPC (Berger/Tielman) is normally 'smoother' as Justin says. Maybe someone has a reference for the updates. Tim Sirk -- gmx-users mailing listgmx-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
SV: [gmx-users] Order parameter for unsaturated lipid chain in UAmodel
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 20.18184 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 listgmx-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 listgmx-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
Re: SV: SV: [gmx-users] Order parameter for unsaturated lipid chain in UAmodel
Sarah Witzke wrote: Thank you for looking at the data. I just thought, that it deviated too much from published results, but perhaps it is because I have mainly worked with saturated lipids. I calculated the order over the last 117 ns of a 167 ns trajectory (10 ps between each frames), so there should be sufficient data I think. Thank you, Sarah Did you look at the papers I linked earlier? Your results look pretty similar to the data from those papers, which included both experimental and computational information. If you're not used to unsaturated lipids, have a look around the literature - there's lots out there! -Justin Fra: Justin A. Lemkul [mailto:jalem...@vt.edu] Sendt: to 25-02-2010 15:14 Til: Sarah Witzke Emne: Re: SV: [gmx-users] Order parameter for unsaturated lipid chain in UAmodel Sarah Witzke wrote: 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? This all looks pretty normal to me, perhaps a little rocky from insufficient sampling? Usually the curves are a bit smoother, but the plot of these data look very much like the published results for other unsaturated lipids. -Justin Order parameters sn-2 chain POPC* 1 0.176177 20.18184 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 -- 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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee
