next up previous
Next: Partial Solvation by Explicit Up: Matching CHARMM's Electrostatic Approximations Previous: Matching CHARMM's Electrostatic Approximations

No Explicit Solvent (RDIE)

A distance-dependent dielectric coefficient (RDIE: $\epsilon_r = r_{ij}$) has been used to approximate solvent screening without including explicit water molecules. Physically, it's a pretty ugly way to cheat. But if you don't want to include water, it may be the best your simulation package has to offer; it is almost certainly better than using unscreened partial charges in the absence of water. For realistic dynamics, we recommend constant-dielectric (CDIE) simulations with explicit solvation and $\epsilon_r = 1$. The presence of water retards conformational searching, however.

The SHIFt option does a good job of monotonically damping a $1/r^3$ force (RDIE electrostatics) to zero. Use of CTOFnb = 10 Åshould suffice. Although simulations have definitely evolved toward explicit solvation with true Coulombic $1/r^2$ forces (CDIE), RDIE SHIFt is arguably the best choice (in CHARMM) when the inclusion of explicit water remains prohibitively expensive.

Peter J. Steinbach 2010-11-15