[gmx-users] g_order output is mirrored

[Igor Marques]

      Igor Marques


On Tue, May 17, 2011 at 8:04 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Igor Marques wrote:
>
>> dear all,
>>
>> i've been trying to use g_order to analyse the disorder of the chains of
>> POPC model membrane simulations, namely the SCD parameters.
>>
>> one example of "desired" output is this:
>> 5IGl.png http://i.imm.io/5IGl.png - Performance of the general amber
>> force field in modeling aqueous POPC membrane bilayers by Balázs Jójárt
>> Tamás A. Martinek DOI: 10.1002/jcc.20748
>>
>>
>> however, my output, when plotted, presents a looks like mirrored:
>> deuter.png
>> http://i.imm.io/5IGK.png
>>
>>
>> my input index files start with the first carbon after the c=o in each
>> chain, as in the tutorial -
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/tutorial.html
>> if started the other way around, the plot resembles published data...
>>
>> a colleague tried the same process with a DMPC membrane model and his
>> plots are also mirrored.
>>
>> our command line:
>> g_order -f ../TRAJECTORY.xtc -s ../TOPOLOGY.tpr -n INDEX_CHAIN_sn1.ndx -od
>> OUTPUT_SCD.xvg
>>
>> what are we not doing/doing wrong?
>>
>>
> A few questions:
>
> 1. What version of Gromacs is this?
> version 4.5.3
>


> 2. Can you post your .ndx file?
> for sn1 chain:
>
Reading structure file
Going to read 1 old index file(s)

  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

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

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!
>


> 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!
>

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 | (540) 231-9080
>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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