FIG. 11.

CVs for solvent reorganization based on volumetric maps. Snapshot of a hydrophobic cavity containing a varying number of water molecules (a). A volumetric map (red transparent contour) is used to define a continuous variable $N_w$ measuring the number of molecules in the cavity. Trajectory of a short SMD simulation on $N_w$ (red), compared to the number of molecules counted with VMD (blue) (b). PMF of $N_w$, computed over ∼400 ns. The use of gridForces maps (see Sec. XIII) in Colvars allows the development of methods for enhanced sampling of fully dynamic aggregates, such as water densities and lipid membranes¹⁰³ (c).