Figure 2. Salt bridge formation using both unbiased and enhanced sampling molecular dynamics simulations.

Using the K12–E23 salt-bridge and the CHARMM22*/TIPS3P force field as an example, we compared (A) unbiased simulations with (B) metadynamics simulations. In (B) we also show how the restraint energy acts to avoid that the ion pairs to form excessively long distances. Note that since the metadynamics simulation is biased, the resulting distribution of distances is not expected to be the same until after this bias has been removed. This unbiasing was performed before calculating the free energy profiles in all other figures and analyses.