[gmx-users] Energy calculation problem with molecule leaving the box

Gordan Horvat ghorvat at chem.pmf.hr
Thu Feb 3 15:05:26 CET 2011

I'm doing molecule dynamics of a calixarene in a acetonitrile box with 
pbc, energy groups defined and npT constant. When I extract interaction 
energies with g_energy from edr file I expect them to be pretty much 
constant because I see no significant conformational changes or changes 
in distance between energy groups and that is true for one part of 
simulation when the molecule is completely in the box. But when a 
molecule partially leaves the box energies of interaction for that part 
which is out of the is box is not calculated (bonded or  with other 
energy groups) and interaction energy sometimes drops to 0.000 for a 
period of time even though the distance between groups doesn't change.
I tried extracting energies through rerunning simulation on trajectories 
which were converted with -pbc nojump or -pbc mol -center but that gave 
zero energies all the time.

How can I fix this energy calculation problem?
Gordan Horvat
Laboratory of Physical Chemistry
Department of Chemistry
Faculty of Science, University of Zagreb
Horvatovac 102a
10000 Zagreb
phone: +385-1-4606138
fax: +385-1-4606131

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