[gmx-users] g_order output is mirrored
Justin A. Lemkul
jalemkul at vt.edu
Wed May 18 15:14:03 CEST 2011
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.dragon88 at gmail.com
> <mailto:igor.dragon88 at gmail.com>> wrote:
>
>
> Igor Marques
>
>
> On Tue, May 17, 2011 at 9:42 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at 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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