[gmx-users] g_order for lipid bilayers

[Justin Lemkul]

On 2/20/13 9:41 AM, Felipe Pineda, PhD wrote:
> Hi,
>
> is it possible to apply g_order to a trajectory of a lipid bilayer when the
> carbon atoms of the acyl chains of the lipid molecules for which the SCD should
> be calculated are not numbered consecutively, i.e. the atom numbers
> corresponding to C21-C22-C23-... (sn-2 chain) are eg  23   22 19 ...  and these
> appear in the corresponding group of the index file?
>

Theoretically the bonded structure should be taken from the .tpr file, but you 
should probably do a quick test to be sure (i.e. consecutively numbered topology 
vs. nonconsecutive).

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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