Background: Cationic antimicrobial peptides offer an alternative to conventional antibiotics, as they physically disrupt bacterial membranes, causing cell death. Results: Peptides designed with high hydrophobicity display strong self-association that is minimized by distribution of positive charges at both peptide termini. Conclusion: Balancing peptide hydrophobicity and charge distribution promotes efficient antimicrobial activity. Significance: Routes to optimization of peptide sequences are valuable for devising therapeutic strategies.