[gmx-users] g_order

[Justin Lemkul]

On 9/10/15 1:58 PM, Stella Nickerson wrote:
> I have a molecule with a carbon chain attached to a ring. I want to use
> g_order to generate the ordering parameter across the simulation box. I've
> read the manual entry for g_order, and it said to create an index file with
> only the "relevant" atoms included, so I made a group with just the atoms
> in the carbon chain and put it in an index file on its own with no other
> groups.
>
> The output file doesn't have any profile in it. It says the x axis is
> "Atom" which I don't want--I want the x axis to be "z" and the y axis to be
> "Sz."
>
> I've been playing with the arguments but nothing I try seems to make a
> difference.
>
> What am I doing wrong?
>

Without seeing your command(s), hard to say, but in principle you should be able 
to get this with some combination of -sl -szonly, etc.  Normal usage of g_order 
is for alkyl chains of membranes, to calculate deuterium order parameters.  I'm 
not clear if that's what you actually want.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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