[gmx-users] Energy calculation problem with molecule leaving the box
Mark.Abraham at anu.edu.au
Fri Feb 4 05:04:54 CET 2011
On 4/02/2011 1:05 AM, Gordan Horvat wrote:
> 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?
So, having run your original simulation with pre-defined energy groups,
starting from the mdrun output files, what commands reproduce your
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