[gmx-users] g_order output is mirrored

[Justin A. Lemkul]

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?

>     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.

>  
> 
>     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> | (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

========================================