I've since found the source of my problem - the program was measuring the (marginally shorter) distance across the PBC boundary, rather than the distance within the box. Unfortunately there doesn't seem to be a way to turn PBC images off (correct me if I'm wrong?), so I guess I'm going to do some jiggerypokery with the data and some math.
Use g_energy to output the box-Z then the distance you want should be the box-Z minus the distance you get. This would be super-dangerous unless you can be sure that it is actually measuring the distance across the boundary each time. If, for instance, it measures the distance you want one time and the distance across the PBC the next time, then Mark's suggestion would be the way to go.
Chris. ----- Original Message ----
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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