[gmx-users] g_dist producing inconsistent values

[chris.neale at utoronto.ca]

>> 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.

I just realized that you could also use g_density, scripted to run  
frame by frame if you need to, and average the histograms yourself.