[gmx-users] g_dist producing inconsistent values
anoddlad at yahoo.com
Thu Feb 7 14:44:37 CET 2008
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.
----- 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...
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