FIGURE 1.

An illustration of the structure of the indole molecule, showing the two sets of partial charges used in our simulations of indole and benzene (in addition to uncharged simulations). Charges are in units of |e|. The partial charges in charge set 1 are adapted from the partial charges in the G96 force field (48) used for the trp side chain. The partial charges in charge set 2 are taken from the ab initio calculations of Woolf et al. (26). The diagram also indicates the local frame used to compute the indole orientation with respect to the bilayer normal (Fig. 8). The z axis is given by the cross product of the x and y axes.