Hi Justin, I used the below g_select command to get the list of phosphorus atoms (from DPPC lipid) within 0.5 nm of protein.
g_select -f ordered.xtc -n initial.ndx -on select.ndx -select "name P and within 0.5 of group Protein" -s md_500ns.tpr -b 100000 -dt 1000 My output is an index file which contains different phosphorus atom number at each frame within 0.5nm of protein and this number changes for every frame. Please can I know if its possible to use this index file to convert each frame into trajectory file and do analysis for lipids within 0.5 of 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: 17 October 2011 20:25 To: Discussion list for GROMACS users Subject: Re: [gmx-users] lipid membrane slicing Poojari, Chetan wrote: > Hi Justin, > > Using make_ndx on the trajectory file (output from trjorder), and listing > out different lipids i did see the lipids arranged based on the distance from > protein. > > Now i want to choose lipids within 0.5nm from protein for my analysis. As in > the index file the lipids are listed based on distance, I am not sure which > lipid numbers fall within 0.5 nm range. > g_select can tell you this. > Please can i know if i can get information about the distance between 1st > lipid listed in index file and the protein, then the 2nd lipid and protein > and so on. > > Either use g_select or measure distances with g_dist. -Justin > Kind Regards, > chetan > > ________________________________________ > From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf > Of Justin A. Lemkul [jalem...@vt.edu] > Sent: 14 October 2011 12:44 > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] lipid membrane slicing > > Poojari, Chetan wrote: >> 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. >> >> > > All the lipids are ordered, not just the ones within 0.5 nm. The -r option is > only useful in conjunction with -shell, for printing the molecules within the > specified distance. Here, it's not doing anything. > >> 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. >> >> > > Use index groups specifying different lipids. They are ordered in the > trajectory by distance, so as the molecule number (and thus atom indices) > increase, so too does that molecule's distance from the protein. > > -Justin > >> 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 >> > > -- > ======================================== > > 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 > > ------------------------------------------------------------------------------------------------ > ------------------------------------------------------------------------------------------------ > 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 > ------------------------------------------------------------------------------------------------ > ------------------------------------------------------------------------------------------------ > -- ======================================== 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? 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