In the Fragment_Placement subroutine, nrg_kBT for a CBMC dihedral trial is compared against max_kBT. If nrg_kBT >= max_kBT, the trial weight is set to zero but overlap is not flagged for the trial. If all the trials have overlap (whether they are flagged as such or not), the first trial is chosen because the cumulative weight for trial 1 is zero, and Cassandra finds that prob_pick <= weight(1) because prob_pick also equals zero. For molecules with multiple fragments, this means that Build_Molecule can grow some molecules with overlap without flagging cbmc_overlap.
In the
Fragment_Placementsubroutine,nrg_kBTfor a CBMC dihedral trial is compared againstmax_kBT. Ifnrg_kBT >= max_kBT, the trial weight is set to zero but overlap is not flagged for the trial. If all the trials have overlap (whether they are flagged as such or not), the first trial is chosen because the cumulative weight for trial 1 is zero, and Cassandra finds thatprob_pick <= weight(1)becauseprob_pickalso equals zero. For molecules with multiple fragments, this means thatBuild_Moleculecan grow some molecules with overlap without flaggingcbmc_overlap.