[gmx-users] Total energy with different energy groups

[Daniel Cheong]

Hi Mark,

Thanks for all your replies and suggestions!  I really appreciate it.  

The observations are indeed inconsistent and that is why I am quite 
confused.  I am not changing anything in my mdp file except for the 
energy groups.  I literally use the same file and just add/change/remove 
the line for the energy group, save the file and run the calculation 
again with a different output filename.  I don't even touch any of the 
cutoff or neighbor list generation frequency or any of the other 
parameters.  In fact I am not even running any MD on it.  I am just 
calculating the initial energy of the configuration.  Hence my surprise 
when I find the total and non-bonded energies turn out different.

Daniel


Mark Abraham wrote:
> Daniel Cheong wrote:
>> 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?
>
> Your observations are inconsistent. 1-4 interactions should be just as 
> reproducible as bonded ones, since they too depend only on the 
> topology and configuration. If the other non-bonded interactions 
> aren't reproduced then I can only suppose you are also changing your 
> cut-offs, or neighbour list generation frequency or some such. Use 
> diff on your .mdp files. Use mdrun -rerun.
>
> Mark
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