I want to know how and where is data of ssd file used?
Actually I have 5 peptide that has been coarse grained with martinize.py. martinize.py takes itp file and ssd file. but in next commands, we use topol.top that includes itp file just. how and where will be called ssd file ?
and another question: is it different that I use one gro file include 5 peptide and then I do coarse graining step (1 itp file and 1 ssd file) or I use 5 gro file to coarse graining (it takes 5 itp file and 5 ssd file)?