[gmx-users] g_dist producing inconsistent values

chris.neale at utoronto.ca chris.neale at utoronto.ca
Thu Feb 7 19:29:54 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.

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.


----- 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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