[gmx-users] Regarding g_order

[Venkat Reddy]

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*)?


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
>
> ==============================**====================
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
> * Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
> * Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>



-- 
With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
Chennai
INDIA-600036