g order

The g_order program calculates order parameters for carbon atoms along an acyl chain, most often a membrane lipid. A common mistake that users make is preparing the index file incorrectly. The index file must specify the carbon atoms of a single acyl chain (sn-1 or sn-2). For example, if you are analyzing DPPC from Tieleman's site:

make_ndx -f dppc128.pdb -o sn1.ndx
> a C34
> a C36
> ...
> a C50
> del 0-2
> q

In the above example, the individual types of carbon atoms along the sn-1 chain are specified, and the standard groups in the index file (System, DPPC, SOL) are deleted.