[gmx-users] Total energy with different energy groups

[Daniel Cheong]

well...  the bonded energies are the same, but the 1-4 and nonbonded 
interactions are different, especially the coulomb-sr energy.  I am 
using a direct summation method with no cutoffs to calculate the 
electrostatic energy.  But the method is consistent between the runs.  
So that shouldn't matter should it?



Mark Abraham wrote:
> Daniel Cheong wrote:
>> Thanks for your reply.  I thought so too, but i have checked it 
>> several times.  The only thing i changed was the "energygrps  ="  
>> line in my .mdp file.  Then the inclusion and exclusion of energy 
>> monitor groups or just specifying different energy groups will result 
>> in a different total energy.  And the larger the energy group, the 
>> greater the difference when compared to the energy calculated with no 
>> energy monitor groups.   i use the exact same initial configuration, 
>> topology, index files.
>
> If you use gmxdump to compare your two energy files, what do you get?
>
> Mark
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