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

[Gordan Horvat]

I extracted trajectories with -pbc center -mol to obtain ones with 
molecules that form different energy groups in all combinations and then 
rerunned the simulation. This procedure was described here 
http://lists.gromacs.org/pipermail/gmx-users/2007-October/030104.html
I seem to get a reasonable interaction energy throughout the simulation 
and no zeroes. Is this a good procedure to calculate interaction energy? 
The reason why I am doing energy calculations posteriori is that a 
solvent molecule enters the calixarene cavity but I don't know which one 
is doing that until after the simulation.
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Subject: Re: [gmx-users] Energy calculation problem with molecule leaving
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