Solvation of the folded and unfolded structures
Solvation can be done using a similar procedure to that described in Step 8 of the PDB Files tutorial. This involves: (i) determining the size of the solvent box to use for each of the proteins; (ii) generating water boxes of the appropriate size; (iii) adding counterions to each of the structures; and (iv) superimposing the protein/counterion and water box systems.
These programs follow the procedure outline above although, to avoid storing partially-constructed systems, the program
SolvateSystem.py combines the last two steps of adding counterions and creating the full solvated systems. In the examples, a single cubic, solvent box is created with box side of length 28 Å. This is quite small and was chosen so as to reduce the times required for the subsequent molecular dynamics simulation. Likewise, the length of the molecular dynamics simulations used to refine the solvated structures is kept to a minimum. More rigorous studies would use larger boxes and longer simulation times.