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 <jalem...@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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Justin A. Lemkul, Ph.D.
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Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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