[gmx-users] g_order output is mirrored

[Igor Marques]

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:
[image: 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:
[image: 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?

best regards and thanks in advance!

      Igor Marques
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110517/fb35ea54/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: deuter.png
Type: image/png
Size: 5427 bytes
Desc: not available
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110517/fb35ea54/attachment.png>