[gmx-users] Regarding g_order

Venkat Reddy venkat4bt at gmail.com
Fri Aug 2 08:04:27 CEST 2013

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

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