I have been asked to include an additional (third) (hydroxide) reaction to the cross-linking "Create Polymer Network" protocol. Is it possible to do so by copying and pasting in the input prompts or are more substantial changes required? Any advice as to how to achieve this would be appreciated.

A second question related to the same protocol. The protocol has three pipelines 1,2, and 3. The first pipeline builds an amorphous cell from the specified monomers and then equilibrates it using NPT/NVT dynamics. The second pipeline then unpacks the xtd trajectory file and passes it to the cross-linking server-side Perl script. The third pipeline then takes the output of the second pipeline and generates statistics. I am curious if I can chop off the first pipeline and simply submit to the revised script an already fabricated amorphous cell that would then be cross-linked. Is this easy to do? I am not sure how all of the variables are initialized, but I recall that the glass transition scripts provide similar functionality.

Any help?