[gmx-users] The sign of deuterium order parameter calculated by g_order

[Jason Zhu]

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