[gmx-users] Total energy with different energy groups

Maik Goette mgoette at mpi-bpc.mpg.de
Tue May 29 10:46:06 CEST 2007

Random velocities?


Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Tel.  : ++49 551 201 2310
Fax   : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/

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.
> Mark Abraham wrote:
>> Daniel Cheong wrote:
>>> Hi,
>>> I am trying to calculate the initial energy of some molecular 
>>> configuration that I have.  I have also defined some energy groups.  
>>> This gives me a set of energy values.  However when I changed the 
>>> energy monitor groups, and repeat the calculation on the same 
>>> configuration, i get a different total energy.  This seems strange to 
>>> me.  I was under the impression that while the mutual interactions of 
>>> the energy groups will of course be different, the total energy of 
>>> the system should be the same regardless of what energy groups I 
>>> define.  Is that right, or am i missing something altogether?  Thanks 
>>> for any help.
>> Probably you're not doing the same calculation. You are right, in that 
>> the energy monitor groups will not affect the calculation of the total 
>> energy.
>> Mark
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