[gmx-users] g_order

[Justin Lemkul]

On 9/10/15 6:58 PM, Stella Nickerson wrote:
> 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
> argument."
>

All GROMACS boolean options are either -option or -nooption, so in this case it 
is -szonly or -noszonly.  The default is -noszonly.

-Justin

>
>
> 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
>> 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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-- 
==================================================

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

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