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
--
========================================
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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