[gmx-users] Order Parameters for alkyl chain

[Justin Lemkul]

On 4/22/15 11:51 AM, Sylvester Tumusiime wrote:
> Dear gromacs users,
>
> I am new to gromacs and i am trying to determine the order parameter for my
> lipid alkyl chain carbon atoms.
>
> I had a pdb file containing co-ordinates for a number of individual lipid
> monomers that i performed the g_order command on to obtain a .ndx file.
>
> At this point i have a .ndx file that i am not quite sure what to do with in
> order to have meaningful insights.
>

I would argue that a single snapshot of a bilayer isn't inherently meaningful, 
anyway.  If you've got the .ndx file, running gmx order is trivial.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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