Are Current Atomistic Force Fields Accurate Enough to Study Proteins in Crowded Environments?
Figure 2
Aggregation of wild-type and carbonylated villin headpiece under various simulation conditions for GROMOS 45a3 and 54a7 force fields.
Percentage of free monomers in solution and the number of intermolecular atomic contacts as a function of time, averaged over independent simulations performed under the same conditions. Altogether, 10 simulation setups were examined and are here grouped according to length: A) 50-ns-long, B) 100-ns-long, and C) 200-ns-long simulations. Exact simulation setup is given above each plot including the force field (GROMOS 45a3 or 54a7), type of electrostatics treatment (RF – reaction field, PME – particle mesh Ewald), protein concentration ([p.]), salt concentration ([NaCl]) and the number of replicate trajectories used to generate the curves (1× or 3×).