[gmx-users] Energy calculation problem with molecule leaving the box
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?
Laboratory of Physical Chemistry
Department of Chemistry
Faculty of Science, University of Zagreb
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