a simulation for each dipeptide ( in their zwitterionic form ) was set up using the gromacs molecular dynamics package . a cubic box with 300 dipeptides , placed randomly with a minimum distance of 3  between them , was solvated in standard martini cg water ( four water molecules per bead ) to a final concentration of 0.4 m. a berendsen thermostat and barostat were used to keep the temperature at 303 k and pressure at 1 bar , respectively . bond lengths in aromatic side chains and the backbone  side - chain bonds in i , v , and y were constrained using the lincs algorithm . all boxes were energy minimized using the steepest descent integrator and then equilibrated for 4  10 time steps of 25 fs . the extended ff simulation was performed in duplicate , and reported tube sizes were averaged over 10 different positions in either simulation . for all experimentally studied dipeptides , a similar simulation over 40  10 steps was performed to study the effect of a longer simulation on the ap . the total screening simulation time equates to 100 ns , but because of the smoothness of the cg potentials , this roughly equates to an effective 400 ns of atomistic simulation time . throughout this letter , all times refer to the simulation time speeded up by this factor of 4 . the size of our systems , the time scales required , and the number of systems that are assessed in a virtual screen excludes the possibility of performing these md simulations using all - atom models on modest computing resources . the complete , 400 ns simulation for a single dipeptide system described above can be carried out in ca . 4 h on a four - core 2.6 ghz opteron compute node . more details of the simulation can be found in the supporting information .