gmx_rmpbc and periodic molecules
gmx_rmpbc should not try to make periodic molecules whole.
gmx_rmpbc currently only gets t_idef passed, not t_inputrec,
so it can not know if periodic molecules are present.
Since gmx_rmpbc gets called 50 times, I do not want to do such
a large change in the beta release stage.
We should fix this properly by having a single trajectory reading class
that also determines the consistency of the tpr and trx file.
#1 Updated by Erik Lindahl over 9 years ago
I think we discussed this before, but I can't remember why it's really necessary to have the entry in the inputrec. Couldn't we simply construct a bond graph to automatically determine whether there are periodic molecules that undergo a net non-zero box shift before connecting back to the first atom?