Thank you Justin, Igor for your suggestions. I tried with trjorder and below is the command i used:
trjorder -f *.xtc -s *.tpr -n order.ndx -na 50 -da 0 -r 0.5 -o ordered.xtc I choose protein as my reference group and lipids as the group of molecules to be ordered, -na 50 : no of atoms in lipid molecule and cut-off distance of 0.5nm from protein. As i understood from trjorder description, the above command i have used should order lipids within 0.5nm from the protein and this information will be outputted into new xtc file i am writing. Using the new xtc file with g_order i should be able to calculate order parameter for lipids within 0.5nm from protein. Please can I know if I am right with the understanding of the trjorder description. Is it possible to order the lipids away from the protein using trjorder, so that i can calculate the order parameter for lipids away from protein as well. If so please can I know how can i set distance away from protein. Kind Regards, chetan ________________________________________ From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul [jalem...@vt.edu] Sent: 11 October 2011 23:24 To: Discussion list for GROMACS users Subject: Re: [gmx-users] lipid membrane slicing Igor Marques wrote: > chetan, > > i'm not sure about the use of -sl option in g_order. > > however, for the purpose you mentioned, i'd suggest you to: > create two different trajectories, using trjconv and an index file > grouping lipids closer to the protein and lipids away from the protein. > then, you should be able to analyse each trajcetory and get the order > parameters for each group of lipids. > This is more easily accomplished with trjorder. -Justin > good luck, > igor > > > Igor Marques > > > On Tue, Oct 11, 2011 at 6:20 PM, Poojari, Chetan > <c.pooj...@fz-juelich.de <mailto:c.pooj...@fz-juelich.de>> wrote: > > Hi, > > I have protein completely inserted into lipid membrane and would > like to study order parameter around the protein as well as away > from the protein. > > For this I would like to slice my membrane into parts. > > I tried the following command: > > g_order -s *.tpr -f *.xtc -n sn1.ndx -d z -od deuter_sn1.xvg -sl 2 > > The output i get from this is as same as the one where i dont use > -sl 2 flag and it also doesnt show the different parts it has used > for order parameter calculation. > > Please can I know how to slice my lipid membrane so that i can study > order parameter for each part separately. > > > Kind Regards, > chetan > > > ------------------------------------------------------------------------------------------------ > > ------------------------------------------------------------------------------------------------ > Forschungszentrum Juelich GmbH > 52425 Juelich > Sitz der Gesellschaft: Juelich > Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 > Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher > Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), > Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, > Prof. Dr. Sebastian M. Schmidt > > ------------------------------------------------------------------------------------------------ > > ------------------------------------------------------------------------------------------------ > -- > gmx-users mailing list gmx-users@gromacs.org > <mailto:gmx-users@gromacs.org> > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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 > <mailto:gmx-users-requ...@gromacs.org>. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > -- ======================================== 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists