Thank you David, I have filled a bugzilla. ________________________________
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/> _______________________________________________ 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! 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