Non Bonded Interaction

Non Bonded  van der Waals Interactions

A cut-off always introduces a discontinuity in both the force and potential energy near the cut-off zone. This creates a problem since energy conservation is a must. One of the alternative is to use a shifted potential where a constant term is subtracted from the potential at all points[Leach,2001]. For e.g

Here v(c) is the potential at cut-off radius. Another alternative is to use a switching function .This is a polynomial function of the distance with which the potential energy function is multiplied i.e

One such function can be written as:

It has the values of 1 at r=0 and 0 at r=r_c.

The non bonded van der Waals interactions are always truncated at the cutoff distance (R_c).The main option that affects van der Waals interactions is the switching parameter. With this option set to ON( i.e in NAMD) , a smooth switching function will be used to truncate the van der Waals potential energy smoothly at the cutoff distance. A graph of the van der Waals potential with this switching function is shown in Figure 14. With the switching function active, the potential is smoothly reduced to 0 at the cutoff distance. Without the switching function, there is a discontinuity where the potential is truncated. Thus, the value of switchdist (R_s) must always be less than that of cutoff.

 Figure 14. Effect of Non Bonded Interaction without/with switching (Adapted from the NAMD user guide: http://www.ks.uiuc.edu/Research/namd/2.9/ug.pdf)