[MMTK] Partial energy computation

[Dmitriy Morozov]

Hi,

Why does the following happen? When I run the code (attached) the 
time that it takes to compute the energy for each half of the 
atoms of the protein is almost the same as for the whole 
protein, and the time that it takes to compute the energy for 
"between the two halves" is almost 4 times the time it takes to 
compute the energy for the whole? In other words, the code 
(attached) outputs the following:

2753.09 + 2539.67 + -299.20 =? 4993.56
Time as a whole 5.82455992699
Time for the first set 4.44697904587
Time for the second set 4.27810192108
Time for between the sets 23.5806781054

Why does this happen and is there any way to "fix" this - if such 
a fix is possible? The timing results are very counter-intuitive 
- am I missing something?

Thanks.
Dmitriy
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