Equilbration of cyclic peptides with disulfide linkages has proved to be difficult. We combine configurational bias Monte Carlo (CBMC) techniques with molecular dynamics and investigate the problem using the hybrid Monte Carlo (HMC). Solvent effects are accounted through solvent accessible surface area and parameter optimized surfaces (POPS) methods. Parallel tempering technique is applied to speed up the equilibration. The peptides of interest are end to end connected cyclic compounds comprising of 30-50 amino acids. Three disulfide bonds forming a cystine-knot is a peculiar feature of the molecules, resulting in slow equilibration. These peptides are known to exhibit specific and potent activity against various pathogens. The hybrid algorithm is expected to facilitate equilibtration significantly better than the existing non-ergodic method.