A question about the periodic boundary condition

[Hang LYU]

Dear developers and users,

   I am now not very clear of the periodic boundary condition in plumed. For example, I am using the COORDINATION function of plumed to calculate the cordination number of atom A. In the periodic simulation box, r_AB is larger than the cut-off distance, however, when we consider the distance between atom A and the replica (B') of atom B in the neighboring box, r_AB' is smaller than the cut-off distance. My question is whether atom B will be considered inside the first coordinate sphere of atom A by plumed.

Regards,

Hang LYU

[Giovanni Bussi]

Hi,

with or without cutoff, by default COORDINATION will use the distance with the closest image (r_AB' in your picture), unless you override this default behavior with NOPBC. Then, that distance might be compared with the cutoff D_MAX to know if it should be ignored

Giovanni

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[Hang LYU]

Thank you very much