I've been using g_dist to plot distances along the normal to my bilayer between
groups. Namely in this case, between the phosphates of opposing leaflets, and
the peptide.
I would expect the sum of the distances between the peptide and each leaflet's
phosphates to equal the distance between the two sets of phosphates. But they
mysteriously don't. I'm taking the z-distance to be the final value in each
row, as the headers in the .xvg indicate:
@ s0 legend "|d|"
@ s1 legend "d\sx\N"
@ s2 legend "d\sy\N"
@ s3 legend "d\sz\N"
0.0000000 3.2837145 0.0671294 -0.0351439 -3.2828403
The index groups are definitely correct (doublechecked by using trjconv -n
-dump and visualising the groups so selected), so there's no error there, I'm
sure. And these are the numbers I get out for the first frame:
Peptide - leaflet 1 phosphates: -3.3361144
Peptide - leaflet 2 phosphates: 0.2953452
Leaflet 1 - leaflet 2 phosphates: -3.2828403
Is there an error in my understanding of how this is working? I'm pretty
certain the first two numbers should sum to the value of the third number.
Alternatively, any idea what could be going wrong? The files being used are
definitely the same, too...
Alan.
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