Anomaly in rdf result

[lauraf244]

Hello,

i have performed a LAMMPS simulation and one of the rdf i'm plotting (between one H atom of menthol and one O atom of acetic acid) is strange. Where is the error?

[orbeckst]

Do you know which atoms are involved? Then I'd visualize the trajectory to see if anything odd is happening.

Alternatively, calculate the distance time series to find frames where the distance is short. You can use MDAnalysis.lib.distances.calc_bonds() for these distance calculations (with PBC). Or use analysis.distances functions or the analysis.atomicdistances.AtomicDistances analysis class.