[gmx-users] Regarding g_order

Justin Lemkul jalemkul at vt.edu
Thu Aug 1 19:24:40 CEST 2013

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 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


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