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: [email protected] på vegne af Sarah Witzke
Sendt: ti 03-03-2009 11:37
Til: [email protected]; 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: [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/>
<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
========================================
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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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