Hi,

      I am trying to implement a dynamics run on each member of a small virtual library of cyclic peptoids I generated in pipeline pilot. What I would ultimately like to do is generate a dcd file (or better yet a combined dsv file with the dcd trajectories loaded for each entry) for each of the library members. I have attached the protocol I was using initially however it returns only a single conformation for each member (and often a rather dubious one) and I cannot figure out how to have the Dynamics Cascade component generate the DCD files for the entries. 

Ultimately I would like to be able to use the dynamics cascade to generate structures for the library that I have confidence in and can use for pharmacaphore screening on this and future libraries. Any input would be much appreciated.

-Cameron