SV: [gmx-users] g_order version 4.0.x

Mon Mar 2 11:45:44 CET 2009

Thank you David, I have filled a bugzilla.
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Fra: gmx-users-bounces at gromacs.org 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.
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> 
>
> Sarah
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>
> ________________________________
>
> Dear Gromacs Users,
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> 
>
> 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:
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> 
>
> g_order -f dmpclim3-all.xtc -n dmpc_order_2.ndx -s dmpclim3-1.tpr -b 100000 -od dmpclim3_order_2.xvg
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> 
>
> 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)
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> After reading that I also tried to specify all carbons in one single group and then run g_order again:
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> 
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> g_order -f dmpclim3-all.xtc -n dmpc_order.ndx -s dmpclim3-1.tpr -b 100000 -od dmpclim3_order_2.xvg
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> 
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> 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
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> There is one group in the index
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> Reading frame       0 time 100000.008
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> Back Off! I just backed up sg-ang.xvg to ./#sg-ang.xvg.1#
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> 
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> Back Off! I just backed up sk-dist.xvg to ./#sk-dist.xvg.1#
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> Reading frame   11000 time 210000.016
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> 
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> Again I only got sg-ang.xvg and sk-dist.xvg but not the wanted deuterium order .xvg file.
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> 
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> 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?
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> I tried g_order version 4.0.3 (again with the index file with only one group):
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> g_order -f dmpclim3-all.xtc -n dmpc_order.ndx -s dmpclim3-1.tpr -b 100000 -od dmpclim3_order_3.xvg
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> 
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> Taking z axis as normal to the membrane
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> 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
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> 
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> Reading frame       0 time 100000.008   Number of elements in first group: 3584
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> Reading frame   11000 time 210000.016
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> 
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> Read trajectory. Printing parameters to file
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> 
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> 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:
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> 
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> dmpclim3_order_3.xvg:
>
> # This file was created Sat Feb 28 20:02:09 2009
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> # 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
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> #
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> # g_order is part of G R O M A C S:
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> #
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> # Great Red Oystrich Makes All Chemists Sane
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> #
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> @    title "Deuterium order parameters"
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> @    xaxis  label "Atom"
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> @    yaxis  label "Scd"
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> @TYPE xy
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> 
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> 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
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> #
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> # g_order is part of G R O M A C S:
>
> #
>
> # Great Red Oystrich Makes All Chemists Sane
>
> #
>
> @    title "Order tensor diagonal elements"
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> @    xaxis  label "Atom"
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> @    yaxis  label "S"
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> @TYPE xy
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> 
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> 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.
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://folding.bmc.uu.se <http://folding.bmc.uu.se/> 
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