[gmx-users] pbc atom

chris.neale at utoronto.ca chris.neale at utoronto.ca
Tue Aug 24 19:04:40 CEST 2010

Dear Gavin:

What happens if you replace your reference group by a single water  
molecule and your pulled group by a single water molecule and run the  
2.35 nm simulation again. Do you get the same two-peaked histogram?  
What about if you use a system with a single water for the reference  
and your regular pulled group?

You should not need to run 100 ns to get an idea about the shape of  
that histogram so it should be a quick test. This is usually how I  
figure things out -- see how much I can reduce the complexity and  
maintain the problem.


-- original message --

Hi Chris

I have generated a histogram from the my.data file and i get a histogram
with the exact same profile as that generated from g_wham. Also on
comparison of the dx, dy, dz values in the g_dist file with the vaules
in the pullx.xvg file I notice that the magnitudes of the vectors are
identical but their signs are opposite. e.g.
g_dist file
-2.2756047   -0.0369981    0.3126130

pullx.xvg file
2.2756  0.036998        -0.312613



Please note that there is a significantly more interaction between the
molecules below 2 nm whereas above they interact very weakly (from
viewing the trajectories)

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