[gmx-users] Total energy with different energy groups

Mark Abraham Mark.Abraham at anu.edu.au
Tue May 29 07:10:40 CEST 2007

Daniel Cheong wrote:
> 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.

Well, start fresh and keep a record of exactly what you do, don't 
over-write any files. If you can reproduce this finding in this way, 
tar+gz all of that up and put it on a website and someone may look at it 
for you.


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