Non-bonded interactions - 非键接相互作用（NAMD）

Non-bonded interactions

NAMD has a number of options that control the way that non-bonded interactions are calculated. These options are interrelated and can be quite confusing, so this section attempts to explain the behavior of the non-bonded interactions and how to use these parameters.

 

Van der Waals interactions

The simplest non-bonded interaction is the van der Waals interaction. In NAMD, van der Waals interactions are always truncated at the cutoff distance, specified by cutoff. The main option that effects van der Waals interactions is the switching parameter. With this option set to on, 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 1. If switching is set to off, the van der Waals energy is just abruptly truncated at the cutoff distance, so that energy may not be conserved.

 

Figure 1: Graph of van der Waals potential with and without the application of the switching function. 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.

The switching function used is based on the X-PLOR switching function. The parameter switchdist specifies the distance at which the switching function should start taking effect to bring the van der Waals potential to 0 smoothly at the cutoff distance. Thus, the value of switchdist must always be less than that of cutoff.

 

Electrostatic interactions

The handling of electrostatics is slightly more complicated due to the incorporation of multiple timestepping for full electrostatic interactions. There are two cases to consider, one where full electrostatics is employed and the other where electrostatics are truncated at a given distance.

 

 

First let us consider the latter case, where electrostatics are truncated at the cutoff distance. Using this scheme, all electrostatic interactions beyond a specified distance are ignored, or assumed to be zero. If switching is set toon, rather than having a discontinuity in the potential at the cutoff distance, a shifting function is applied to the electrostatic potential as shown in Figure 2. As this figure shows, the shifting function shifts the entire potential curve so that the curve intersects the x-axis at the cutoff distance. This shifting function is based on the shifting function used by X-PLOR.

 

Figure 2: Graph showing an electrostatic potential with and without the application of the shifting function.

Next, consider the case where full electrostatics are calculated. In this case, the electrostatic interactions are not truncated at any distance. In this scheme, the cutoff parameter has a slightly different meaning for the electrostatic interactions -- it represents the local interaction distance, or distance within which electrostatic pairs will be directly calculated every timestep. Outside of this distance, interactions will be calculated only periodically. These forces will be applied using a multiple timestep integration scheme as described in Section 7.3.4.

 

Figure 3: Graph showing an electrostatic potential when full electrostatics are used within NAMD, with one curve portion calculated directly and the other calculated using PME.

 

Non-bonded force field parameters

 

• cutoff  local interaction distance common to both electrostatic and van der Waals calculations (Å)  
  Acceptable Values: positive decimal 
  Description: See Section 5.2 for more information.

   

• switching  use switching function?  
  Acceptable Values: on or off 
  Default Value: on 
  Description: If switching is specified to be <