[gmx-users] Regarding g_order

[Justin Lemkul]

On 8/2/13 2:04 AM, Venkat Reddy wrote:
> Thanks Justin for the quick reply. I am simulating a protein with bound
> lipids. I am in a dilemma to choose the direction of the normal to
> calculate order parameter. In your *Membrane-protein *simulation tutorial,
> you have chosen normal to the bilayer along the z-axis. But in my case,
> there is no bilayer, infact, only few bound lipids are there. In which
> direction I should choose the normal (*-d option*)?
>

You'll probably have to do some sort of reorienting of the molecules for the 
results to make sense.

-Justin

>
> On Thu, Aug 1, 2013 at 10:54 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 8/1/13 12:07 PM, Venkat Reddy wrote:
>>
>>> Dear Gmx-users,
>>> In the GROMACS site, it has been mentioned that there is a bug (Instead of
>>> numbering carbons from 2-17, the numbering starts from 1-16) in g_order
>>> program up to, and including, v4.5.4. But when I am using v4.5.5, I am
>>> getting the same sort of numbering. Is it normal or I should renumber from
>>> 2-17?
>>>
>>>
>> If you're getting a number starting with 1, it's probably wrong.  You
>> can't calculated Scd for the first carbon in a chain because there is no
>> n-1 carbon from which to determine the necessary vectors.  Someone
>> (probably me) updated the wiki when version 4.5.4 was current, so probably
>> any 4.5.x version is really affected, and 4.6.x may be as well, since this
>> really is just a trivial bug that requires simple reinterpretation.
>>
>> -Justin
>>
>> --
>> ==============================**====================
>>
>> 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 <jalemkul at outerbanks.umaryland.edu> | (410)
>> 706-7441
>>
>> ==============================**====================
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>
>
>

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

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

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