Good idea, I'll try that when I get home next week. -Sarah ________________________________
Fra: [email protected] på vegne af Justin A. Lemkul Sendt: ma 02-03-2009 13:58 Til: Discussion list for GROMACS users Emne: Re: SV: [gmx-users] g_order version 4.0.x Sarah Witzke wrote: > Thank you David, I have filled a bugzilla. > g_order works for me under version 4.0.4, perhaps try an upgrade? -Justin ________________________________ > > Fra: [email protected] på vegne af David van der Spoel > Sendt: ma 02-03-2009 10:55 > Til: Discussion list for GROMACS users > Emne: Re: [gmx-users] g_order version 4.0.x > > > > Sarah Witzke wrote: >> Dear Gromacs users, >> >> >> >> I'm sorry to resend this email but I sent it yesterday (27 hours ago) and I >> still haven't received it myself. I'm sorry for the inconvenience it might >> cause. >> >> >> >> Sarah >> >> >> ________________________________ >> >> Dear Gromacs Users, >> >> >> >> I have simulated a lipid bilayer (128 DMPC molecules) with some small >> hydrophobic molecules. These small molecules go from the water into the >> bilayer and I now want to do some analysis to see, whether this has changed >> e.g. membrane thickness or the order of the lipid tails. I'm new to gromacs >> and this is my first try with analysis. >> >> For analysing the order of the lipid tales, I use g_order. The first index >> file I created consisted of 28 groups - one for each of the 14 carbons >> (including the carbonyl-C) in the two chains. The atoms in each of the 128 >> lipid molecules have the same atom name (e.g. c1, c2...) so each of the 28 >> groups in the index file consist of 128 atoms (an entry in make_ndx would >> look like this "a c15 & r DMPC"). >> >> Then I tried g_order version 4.0.2: >> >> >> >> g_order -f dmpclim3-all.xtc -n dmpc_order_2.ndx -s dmpclim3-1.tpr -b 100000 >> -od dmpclim3_order_2.xvg >> >> >> >> I'm asked to "Select the group that contains the atoms you want to use for >> the tetrahedrality order parameter calculation:" and then all the 28 groups >> are listed. This was not what I had expected; I thought g_order calculated >> the order parameter for all the tail carbons at once. I tried just choosing >> group 0 to see what happened: Not much - as was expected. Two files were >> generated: sg-ang.xvg and sk-dist.xvg. This I found strange since I hadn't >> asked for them, but then I found this bugzilla report: >> http://www.gromacs.org/component/option,com_wrapper/Itemid,157/ >> <https://sdumail.sdu.dk/exchweb/bin/redir.asp?URL=http://www.gromacs.org/component/option,com_wrapper/Itemid,157/> >> (no. 264) >> >> >> >> >> >> After reading that I also tried to specify all carbons in one single group >> and then run g_order again: >> >> >> >> g_order -f dmpclim3-all.xtc -n dmpc_order.ndx -s dmpclim3-1.tpr -b 100000 >> -od dmpclim3_order_2.xvg >> >> >> >> Reading file dmpclim3-1.tpr, VERSION 4.0 (single precision) >> >> Reading file dmpclim3-1.tpr, VERSION 4.0 (single precision) >> >> Select the group that contains the atoms you want to use for the >> tetrahedrality order parameter calculation: >> >> Group 0 >> (C15_&_DMPC_C17_&_DMPC_C18_&_DMPC_C19_&_DMPC_C20_&_DMPC_C21_&_DMPC_C22_&_DMPC_C23_&_DMPC_C24_&_DMPC_C25_&_DMPC_C26_&_DMPC_C27_&_DMPC_C28_&_DMPC_C29_&_DMPC_C32_&_DMPC_C34_&_DMPC_C35_&_DMPC_C36_&_DMPC_C37_&_DMPC_C38_&_DMPC_C39_&_DMPC_C40_&_DMPC_C41_&_DMPC_C42_&_DMPC_C43_&_DMPC_C44_&_DMPC_C45_&_DMPC_C46_&_DMPC) >> has 3584 elements >> >> There is one group in the index >> >> Reading frame 0 time 100000.008 >> >> Back Off! I just backed up sg-ang.xvg to ./#sg-ang.xvg.1# >> >> >> >> Back Off! I just backed up sk-dist.xvg to ./#sk-dist.xvg.1# >> >> Reading frame 11000 time 210000.016 >> >> >> >> Again I only got sg-ang.xvg and sk-dist.xvg but not the wanted deuterium >> order .xvg file. >> >> >> >> So, in the bugzilla report it also said that the problem had been fixed in >> the CVS. Unfortunately I don't know what this is, could anyone explain me >> please? >> >> >> >> I tried g_order version 4.0.3 (again with the index file with only one >> group): >> >> g_order -f dmpclim3-all.xtc -n dmpc_order.ndx -s dmpclim3-1.tpr -b 100000 >> -od dmpclim3_order_3.xvg >> >> >> >> Taking z axis as normal to the membrane >> >> Reading file dmpclim3-1.tpr, VERSION 4.0 (single precision) >> >> Using following groups: >> >> Groupname: >> C15_&_DMPC_C17_&_DMPC_C18_&_DMPC_C19_&_DMPC_C20_&_DMPC_C21_&_DMPC_C22_&_DMPC_C23_&_DMPC_C24_&_DMPC_C25_&_DMPC_C26_&_DMPC_C27_&_DMPC_C28_&_DMPC_C29_&_DMPC_C32_&_DMPC_C34_&_DMPC_C35_&_DMPC_C36_&_DMPC_C37_&_DMPC_C38_&_DMPC_C39_&_DMPC_C40_&_DMPC_C41_&_DMPC_C42_&_DMPC_C43_&_DMPC_C44_&_DMPC_C45_&_DMPC_C46_&_DMPC >> First atomname: C15 First atomnr 44 >> >> >> >> Reading frame 0 time 100000.008 Number of elements in first group: >> 3584 >> >> Reading frame 11000 time 210000.016 >> >> >> >> Read trajectory. Printing parameters to file >> >> >> >> Now two order files are generated: The wanted dmpclim3_order_3.xvg and also >> order.xvg which I didn't request for. (No sg-ang.xvg and sk-dist.xvg this >> time). >> >> Unfortunately neither of the obtained .xvg files contain any order >> parameters: >> >> >> >> dmpclim3_order_3.xvg: >> >> # This file was created Sat Feb 28 20:02:09 2009 >> >> # by the following command: >> >> # g_order -f dmpclim3-all.xtc -n dmpc_order.ndx -s dmpclim3-1.tpr -b 100000 >> -od dmpclim3_order_3.xvg >> >> # >> >> # g_order is part of G R O M A C S: >> >> # >> >> # Great Red Oystrich Makes All Chemists Sane >> >> # >> >> @ title "Deuterium order parameters" >> >> @ xaxis label "Atom" >> >> @ yaxis label "Scd" >> >> @TYPE xy >> >> >> >> order.xvg: >> >> # This file was created Sat Feb 28 20:02:09 2009 >> >> # by the following command: >> >> # g_order -f dmpclim3-all.xtc -n dmpc_order.ndx -s dmpclim3-1.tpr -b 100000 >> -od dmpclim3_order_3.xvg >> >> # >> >> # g_order is part of G R O M A C S: >> >> # >> >> # Great Red Oystrich Makes All Chemists Sane >> >> # >> >> @ title "Order tensor diagonal elements" >> >> @ xaxis label "Atom" >> >> @ yaxis label "S" >> >> @TYPE xy >> >> >> >> I will be very thankful if anyone has any suggestions as to what I'm doing >> wrong? >> >> > Please submit a bugzilla. > I fixed something before 4.0.3, but apparently not everything. > > -- > David van der Spoel, Ph.D., Professor of Biology > Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. > [email protected] [email protected] http://folding.bmc.uu.se > <http://folding.bmc.uu.se/> <http://folding.bmc.uu.se/> > _______________________________________________ > gmx-users mailing list [email protected] > http://www.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 [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > _______________________________________________ > gmx-users mailing list [email protected] > http://www.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 [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- ======================================== Justin A. Lemkul Graduate Research Assistant 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 [email protected] http://www.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 [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php _______________________________________________ gmx-users mailing list [email protected] http://www.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 [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
