Simulated system: hydrophobic walls, 1030 water molecules and two methanelike particles.
Pocket intersection: effective radius and effective volume, measured from the pocket entrance (defined as a surface containing the first layer of wall molecules) to border, where water-wall interaction energy was greater that , Me: methane molecule, and : reaction coordinate used in PMF calculations.
Spatial distribution of: wall-solvent energy , solvent-solvent energy , water density , and solvent energy density . These and all other contour maps were generated with the XFARBE program (Ref. 81).
PMF curves for considered systems. Plots resulting from increasing number of simulation data are shown. Note that base lines are shifted for each plot except the R8.
sPMFs plots (solid line), work component (dotted line), and their difference (dashed line), accompanied by solvent density and solvent energy density contour maps for selected values of the reaction coordinate. Grayscale legends inserted in R8 and R5 plots are common for all cases.
Schematic representation of the molecular surface (MS: thick line) and the solvent accessible surface (SAS: dashed line) of two atoms (gray). An empty circle denotes a solvent sphere used for surface construction.
Comparison of sPMFs (solid lines) with estimations based on SASA and MSA approaches (dashed lines). Note that base lines are shifted for each plot except the R8.
RMSD values for predictions in relation to sPMF for each system.
Force field parameters. (m)—modified parameters for grid. LJ potential from is .
Properties of systems used in PMF calculation. : effective pocket volume; : effective pocket radius; : number of water molecules occupying a pocket volume when standard density is assumed; and : distance between walls.
Detailed values for extrema in PMF curves. CM: PMF value at contact minimum; sCM: solvent induced contribution to CM; DB: solvent induced contribution of PMF at desolvation barrier.
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