Igor Marques wrote:
dear all,
after justin contribution, the SN2 chain plot now looks a little different:
sn2_new.png
http://imm.io/5JAZ
the real matter of this e-mail, although i really appreciate the help
justin has provided regarding the proper use of this tool, is the fact
that my plot looks mirrored from the one i've previously referred, from
Jojart and Martinek --> http://i.imm.io/5IGl.png
forgetting, for now, the SN2 chain, harder to analyse, what i really
found weird is the fact that SN1 is mirroring the published results:
sn1_new.png
http://imm.io/5JCi
so, for segment 2, the first they analyze, in the filled triangle line
the value is around 0.35, while for the 14th segment the value is about
0.28. in my case, the order is the other way around! my SN1 starts with
a low value that is increased through the chain! (0.24 --> 0.29).
should i change the order of the chain in the index files? although that
makes the plot resemble the ones already published, i don't think that
is the definitive solution to this problem!
Definitely not. If you look at the sn-2 chain, even counting backwards doesn't
place the unsaturation in the right place.
Are you sure the membrane hasn't entered a gel phase? Are other parameters
(APL, membrane thickness, density, etc) reasonable for the conditions applied?
I can't reproduce this as a problem in g_order 4.0.7 or 4.5.3 - my POPC
membranes look fine (granted, I've used a different force field than you, but my
results match almost exactly with what Jojart and Martinek show).
If everything else in the data analysis looks normal, I am willing to help you
look into this if you send me (off-list):
1. A coordinate file
2. A .tpr file
3. Any index files you're using
-Justin
(this applies also to the DMPC chains of my colleague)
best regards!
igor
Igor Marques
On Tue, May 17, 2011 at 9:47 PM, Igor Marques <igor.drago...@gmail.com
<mailto:igor.drago...@gmail.com>> wrote:
Igor Marques
On Tue, May 17, 2011 at 9:42 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
Igor Marques wrote:
<snip>
2. Can you post your .ndx file?
for sn1 chain:
Reading structure file
Going to read 1 old index file(s)
Not exactly what I was going for (I wanted to see the contents
of the .ndx file), but...
0 C12_&_r_1-72 : 72 atoms
1 C29_&_r_1-72 : 72 atoms
2 C30_&_r_1-72 : 72 atoms
3 C31_&_r_1-72 : 72 atoms
4 C32_&_r_1-72 : 72 atoms
5 C33_&_r_1-72 : 72 atoms
6 C34_&_r_1-72 : 72 atoms
7 C35_&_r_1-72 : 72 atoms
8 C36_&_r_1-72 : 72 atoms
9 C37_&_r_1-72 : 72 atoms
10 C38_&_r_1-72 : 72 atoms
11 C39_&_r_1-72 : 72 atoms
12 C40_&_r_1-72 : 72 atoms
13 C41_&_r_1-72 : 72 atoms
14 C42_&_r_1-72 : 72 atoms
Here you only have 15 carbons. The sn-1 (palmitoyl) should be 16.
for sn2 chain:
Reading structure file
Going to read 1 old index file(s)
0 C9_&_r_1-72 : 72 atoms
1 C13_&_r_1-72 : 72 atoms
2 C14_&_r_1-72 : 72 atoms
3 C15_&_r_1-72 : 72 atoms
4 C16_&_r_1-72 : 72 atoms
5 C17_&_r_1-72 : 72 atoms
6 C18_&_r_1-72 : 72 atoms
7 C19_&_r_1-72 : 72 atoms
8 C20_&_r_1-72 : 72 atoms
9 C21_&_r_1-72 : 72 atoms
10 C22_&_r_1-72 : 72 atoms
11 C23_&_r_1-72 : 72 atoms
12 C24_&_r_1-72 : 72 atoms
13 C25_&_r_1-72 : 72 atoms
14 C26_&_r_1-72 : 72 atoms
15 C27_&_r_1-72 : 72 atoms
16 C28_&_r_1-72 : 72 atoms
And the same here - 17 groups instead of 18. I'm not familiar
with the numbering, but it seems odd to jump from, e.g., C9 to
C13 - are you sure your first carbon (C9) is not in the glycerol
backbone rather than the ester?
i'll also take a careful look into this! and the numbering is
just like this. don't ask! ;)
3. What is your command for the sn-2 chain? You cannot
obtain
unsaturated and saturated order parameters in the same
command. You
must do them separately, and the index groups are
different. For
instance, to get the order parameters around the
unsaturation, your
index file should contain only Cn-1, Cn, Cn+1, Cn+2,
where Cn and
Cn+1 are the C atoms joined by the double bond. Then run
g_order
with the -unsat option. These values can then replace the
corresponding carbon positions in the g_order output of
the whole
sn-2 chain. If done improperly, you can get weird results.
the command is actually the same with the apropriate
index file...
maybe this is the problem for POPC - i'll look at it
carefully!
Then this is certainly a problem.
i'll look at it with my colleague. if our problem persists,
we'll get back in touch!
thanks again! ^^
4. What are the simulation conditions? Are you trying to
replicate
the published work? Different simulations conditions
will certainly
impact the structural parameters, and insufficient
sampling can give
weird looking curves, as well. All it might mean is that
your data
are not yet well-converged.
NPT, surface tension of 40 dyn/cm, t=310 K, GAFF force
field. the
plot represents the last 10 of 150 ns of production -
however, it
presents the same behavior in longer (200 ns) simulations!
I'd suspect the index file(s) and/or g_order commands rather
than convergence issues, in this case.
-Justin
thanks!
-Justin
best regards and thanks in advance!
Igor Marques
-- ========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> |
(540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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