[gmx-users] Regarding g_order
jalemkul at vt.edu
Fri Aug 2 13:46:42 CEST 2013
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.
> 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
>> 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 <jalemkul at outerbanks.umaryland.edu> | (410)
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Justin A. Lemkul, Ph.D.
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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