[gmx-users] g_order output is mirrored

Igor Marques igor.dragon88 at gmail.com
Tue May 17 20:50:40 CEST 2011

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]

my input index files start with the first carbon after the c=o in each
chain, as in the tutorial -
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
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