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

[Justin Lemkul]

On 12/22/17 10:14 AM, Jason Zhu wrote:
> 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.

https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2017-July/114678.html

-Justin

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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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