Hello Accelrys Community,

I have simulated the same protein for 1ns in 3 different conditions and have three trajectories corresponding to each of those runs. It is my desire to perform an RMSD of protein condition1 vs. protein condition 2 (and eventually 1 vs. 3 and 2 vs 3) that compares frame by frame the trajectories of those two runs. The current set up, under the analyze trajectory function, appears to allow comparison of a trajectory to a static reference frame and not to multiple frames of a separate trajectory. Is there a way to set up the described RMSD analysis above in DS that is currently eluding me? Your advice would be greatly appreciated.

Thank you for your help,

David