[gmx-users] Question regarding g_order

[Justin Lemkul]

On 10/3/13 11:50 AM, sa wrote:
> 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

Remember to renumber the first file so it starts with carbon 2, then make the 
replacements.

> 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?
>

I would suggest you contact the authors directly.  I see the same thing 
frequently from other groups that have used Gromacs, but I cannot ever get the 
same outcome, which seems to indicate to me that they are using a modified 
version of g_order or they are somehow extrapolating their values.  In any case, 
if you figure out how they're doing it, please report back because this is a FAQ 
on this list when it comes to lipid analysis.

-Justin

> -- 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
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

==================================================