SV: SV: SV: [gmx-users] g_order version 4.0.x
Sarah Witzke
sawit02 at student.sdu.dk
Mon Mar 9 23:03:17 CET 2009
My .xtc file is 219.41 ns and therefor I thought to just use the last ~100 ns where my molecules have diffused into the membrane.
I have just run g_order again whitout the -b option: the result is the same, no order parameters.
My index file consists of just one big group. In that groups are the carbon atoms of the two lipid chains (and the two carbonyl carbons) for each of my 128 lipids. When running g_order it reads the .ndx file like this:
/home/nat-mem-sw/sawit02/gromacs-4.0.4/bin/g_order -s dmpclim3-1.tpr -n dmpc_order.ndx -f dmpclim3-all.xtc -od dmpclim3_order_5.xvg
:-) G R O M A C S (-:
GROtesk MACabre and Sinister
:-) VERSION 4.0.4 (-:
Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2008, The GROMACS development team,
check out http://www.gromacs.org <http://www.gromacs.org> for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) /home/nat-mem-sw/sawit02/gromacs-4.0.4/bin/g_order (-:
Option Filename Type Description
------------------------------------------------------------
-f dmpclim3-all.xtc Input Trajectory: xtc trr trj gro g96 pdb cpt
-n dmpc_order.ndx Input Index file
-s dmpclim3-1.tpr Input Run input file: tpr tpb tpa
-o order.xvg Output xvgr/xmgr file
-od dmpclim3_order_5.xvg Output xvgr/xmgr file
-os sliced.xvg Output xvgr/xmgr file
-Sg sg-ang.xvg Output, Opt. xvgr/xmgr file
-Sk sk-dist.xvg Output, Opt. xvgr/xmgr file
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-nice int 19 Set the nicelevel
-b time 0 First frame (ps) to read from trajectory
-e time 0 Last frame (ps) to read from trajectory
-dt time 0 Only use frame when t MOD dt = first time (ps)
-[no]w bool no View output xvg, xpm, eps and pdb files
-[no]xvgr bool yes Add specific codes (legends etc.) in the output
xvg files for the xmgrace program
-d enum z Direction of the normal on the membrane: z, x or y
-sl int 1 Calculate order parameter as function of
boxlength, dividing the box in #nr slices.
-[no]szonly bool no Only give Sz element of order tensor. (axis can
be specified with -d)
-[no]unsat bool no Calculate order parameters for unsaturated
carbons. Note that this cannot be mixed with
normal order parameters.
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 0.000 Number of elements in first group: 3584
Reading frame 21000 time 210000.016
Read trajectory. Printing parameters to file
Back Off! I just backed up order.xvg to ./#order.xvg.3#
Thank you for your very quick reply!
Sarah
________________________________
Fra: gmx-users-bounces at gromacs.org på vegne af Justin A. Lemkul
Sendt: ma 09-03-2009 22:38
Til: Discussion list for GROMACS users
Emne: Re: SV: SV: [gmx-users] g_order version 4.0.x
Sarah Witzke wrote:
> Dear Justin and others,
>
>
>
> I have now tried the exact same command g_order command with the exact same result:
>
> /home/nat-mem-sw/sawit02/gromacs-4.0.4/bin/g_order -s dmpclim3-1.tpr -n dmpc_order.ndx -f dmpclim3-all.xtc -od dmpclim3_order_4.xvg -b 100000
>
How long is the trajectory? Does the command work if you don't use -b? Maybe a
huge skip in time is causing problems, although I don't think it should.
What is in your .ndx file?
>
>
> This gives - again - the wanted file for the deuterium order parameters, dmpclim3_order_4.xvg, and also the non-requested for file order.xvg.
>
Right, order.xvg is generated by default, whether you specify it or not.
-Justin
>
>
> Both files - again - contain no parameters:
>
>
>
>
>
> /data1/PROJECTS/LIMONENE/LIM-BILAYERS/DMPC/3> more dmpclim3_order_4.xvg
>
> # This file was created Mon Mar 9 21:45:17 2009
>
> # by the following command:
>
> # /home/nat-mem-sw/sawit02/gromacs-4.0.4/bin/g_order -s dmpclim3-1.tpr -n dmpc_order.ndx -f dmpclim3-all.xtc -od dmpclim3_order_4.xvg -b 100000
>
> #
>
> # /home/nat-mem-sw/sawit02/gromacs-4.0.4/bin/g_order is part of G R O M A C S:
>
> #
>
> # Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
>
> #
>
> @ title "Deuterium order parameters"
>
> @ xaxis label "Atom"
>
> @ yaxis label "Scd"
>
> @TYPE xy
>
>
>
> /data1/PROJECTS/LIMONENE/LIM-BILAYERS/DMPC/3> more order.xvg
>
> # This file was created Mon Mar 9 21:45:17 2009
>
> # by the following command:
>
> # /home/nat-mem-sw/sawit02/gromacs-4.0.4/bin/g_order -s dmpclim3-1.tpr -n dmpc_order.ndx -f dmpclim3-all.xtc -od dmpclim3_order_4.xvg -b 100000
>
> #
>
> # /home/nat-mem-sw/sawit02/gromacs-4.0.4/bin/g_order is part of G R O M A C S:
>
> #
>
> # Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
>
> #
>
> @ title "Order tensor diagonal elements"
>
> @ xaxis label "Atom"
>
> @ yaxis label "S"
>
> @TYPE xy
>
>
>
> This is driving me crazy. Clearly I must be doing something wrong since it is working for Justin - but what? If anyone has any suggestions they'll be much appreciated!
>
>
>
> Another thing: David van der Spoel asked me to file a bugzilla which I have done. After the email from Justin he wrote to me and asked whether version 4.0.4 was working for me. I wanted to write him back to answer him that I would try this today when I was back from holiday, but every time I tried to email him my email couldn't be delivered. Am I - again - doing something wrong, or do I have bad gromacs karma?
>
>
>
> Best regards and thank you,
>
> Sarah
>
>
> ________________________________
>
> Fra: gmx-users-bounces at gromacs.org på vegne af Sarah Witzke
> Sendt: ti 03-03-2009 11:37
> Til: jalemkul at vt.edu; Discussion list for GROMACS users
> Emne: SV: SV: [gmx-users] g_order version 4.0.x
>
>
>
> Good idea, I'll try that when I get home next week.
>
> -Sarah
>
> ________________________________
>
> Fra: gmx-users-bounces at gromacs.org 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: 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.
>>>
>>>
>>>
>>> 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.
>> spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se <http://folding.bmc.uu.se/> <http://folding.bmc.uu.se/> <http://folding.bmc.uu.se/> <http://folding.bmc.uu.se/>
>> _______________________________________________
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>
> --
> ========================================
>
> 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 gmx-users at gromacs.org
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>
> _______________________________________________
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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