I tried MC simulation to perform conformational sampling of the pentapeptide. I used rigid translation and rotation for the water molecules and cart/tors for peptide. I ran for 90000 steps and when I clustered the trajectory, all were in single cluster. Thus it shows of no good sampling. I used separate MVTP ROT for phi,psi,omega and lastly concerted rotations for the peptide, but even this sampling is not effective. I don't want to perform MCM. Can anyone suggest me which parameter has to be changed for efficient sampling?
Thanks in advance for any comments/suggestions


Ramya.L.