Hi all,
I am trying to compute the order parameters for the sn1 and sn2 chains of
DOPC (CHARMM36) in bilayer . I am using the g_order tool (v4.6.3).
I have constructed for each DOPC chain two index files that contains in
the first one all the Carbon atoms where the first Carbon is C=O and the
last one is the last methyl. The second index file for the unsat
calculations contains only the carbons of the C-C9=C10-C.
I am confused here, since the file obtained from g_order w/o the -unsat
argument contains only 16 values and in case of the file generated with
g_order w the -unsat argument 2 values. I am aware that I need to replace
the 9 -10 values in first by those of the second file. However I would like
to compare my SCD values with those obtained by Jämbeck and P. Lyubartsev
(figure 2 in ref [1] ), The authors present graph for DOPC with 17 values.
How it is possible? Did I miss something, here?
-- g_order w/o unsat
# g_order_mpi is part of G R O M A C S:
#
# GROup of MAchos and Cynical Suckers
#
@ title "Deuterium order parameters"
@ xaxis label "Atom"
@ yaxis label "Scd"
@TYPE xy
1 0.20508
2 0.148241
3 0.184247
4 0.184565
5 0.184457
6 0.166101
7 0.118359
8 0.0774722
9 0.0703466
10 0.0511651
11 0.0977673
12 0.0968413
13 0.100903
14 0.0869513
15 0.0806322
16 0.0602708
-- g_order w/ unsat
# g_order_mpi is part of G R O M A C S:
#
# GRoups of Organic Molecules in ACtion for Science
#
@ title "Deuterium order parameters"
@ xaxis label "Atom"
@ yaxis label "Scd"
@TYPE xy
1 0.104554
2 0.0111027
[1] http://pubs.acs.org/doi/full/10.1021/ct300342n
Thank in advance
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