Dear All,
I am studying the effects of cholesterols in POPC lipid bilayer. The
Gromacs is the version 4.6.5 in my simulations.
By using the g_order, I could output the deuterium order parameter of POPC
lipids for a long-term equilibration.
"g_order_mpi -s msd.tpr -f msd-mol.xtc -n sn1.ndx -d z -od deuter_sn1.xvg
-o order_sn1.xvg"
The results in the file of "deuter_sn1.xvg" are given as below:
@ title "Deuterium order parameters"
@ xaxis label "Atom"
@ yaxis label "Scd"
@TYPE xy
1 0.204493
2 0.223424
3 0.222852
4 0.228435
5 0.230187
6 0.229785
7 0.223191
8 0.217353
9 0.204112
10 0.193993
11 0.176565
12 0.162058
13 0.13807
14 0.112887
As in the experimental papers about the deuterium order parameter measured
by NMR, the Scd is negative and round -0.2.
I understand the sign of the deuterium order parameter is not measurable in
conventional NMR. I am wondering the values calculated and output by
g_order in Gromacs is the absolute value (|Scd|) or the opposite value
(-Scd) by default.
Sorry to bother you with this simple question. But I didn't find any clear
answer from mail list or manual. It would be appreciated if you could give
your insights or comments.
Best,
Wenpeng Zhu
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