Switch for Stochastic Boundary

If TRUE, in accordance with the dissipation-fluctuation theorem, a random force is exerted on all atoms that are subjected to friction. Which atoms are subjected to friction depends on the harmonic restraints set in the coord.lis file (see below) or the setting of the SBOUND parameters.

If you use harmonic restraints only (all SBOUND parameters are set to zero), you can define the friction coefficient for every atom individually (see lis-file coord.lis). If the friction-coefficient of an atom is zero, no friction and no random force acts on that atom.

The utility program xpl2lis uses the nineth column (atom-property Q in X-PLOR) of a PDB file to define the friction coefficient. The EGO distribution includes the X-PLOR-script file $(HOME)/ego/utils/boundary.inp, which demonstrates how to set up friction coefficients for a selection of atoms.

If you use SBOUND, the friction coefficients in the coord.lis file are ignored and instead the stochastic forces act on atoms which are in the SBOUND region or closer then the distance value (in Å) specified in ``Additional stochastic boundary thickness''. The friction coefficient, given in ps<sup>-1</sup>, increases linearly from 0 to the value specified in ``Maximum friction coefficient''. For details see Figure 4.1.