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
<<deuter.png>>
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