[gmx-users] g_dist producing inconsistent values

[Alan Dodd]

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...
>
> Alan.
>
>
>
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