[gmx-users] g_order output is mirrored

Igor Marques igor.dragon88 at gmail.com
Tue May 17 22:47:26 CEST 2011 

      Igor Marques


On Tue, May 17, 2011 at 9:42 PM, Justin A. Lemkul <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> | (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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