[gmx-users] g_order

Stella Nickerson stella.nickerson at gmail.com
Fri Sep 11 00:58:19 CEST 2015

I'm simulating an ionic liquid/water liquid-liquid interface. The IL has an
alkyl chain hanging off a ring, and previous simulations have found
ordering of the IL at the liquid-liquid surface as the molecules
essentially lay themselves flat against the interface. I though Sz might
illustrate that. The interface is perpendicular to the z vector.

I tried a few different commands. The latest was:

g_order_mpi -f mdDone.trr -s md.tpr -n ndx-order.ndx -sl 50 -o order.xvg

I can't figure out how to input the boolean for -szonly. I've tried "yes"
"true" and "1" and it always tells me that's an "invalid command line

On Thu, Sep 10, 2015 at 1:44 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

> 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
> --
> ==================================================
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
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> 20 Penn St.
> Baltimore, MD 21201
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
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