Pair list generation

The last critical parameter for non-bonded interaction calculations is the parameter pairlistdist. To reduce the cost of performing the non-bonded interactions, NAMD uses a non-bonded pair list. This list contains all pairs of atoms for which non-bonded interactions should be calculated. Performing the search for pairs of atoms that should have their interactions calculated is an expensive operation. Thus, the pair list is only calculated periodically, once per cycle. Unfortunately, pairs of atoms move relative to each other during the steps between preparation of the pair list. Because of this, if the pair list were built to include only those pairs of atoms that are within the cutoff distance when the list is generated, it would be possible for atoms to drift closer together than the cutoff distance during subsequent timesteps and yet not have their non-bonded interactions calculated.

Let us consider a concrete example to better understand this. Assume that the pairlist is built once every ten timesteps and that the cutoff distance is 8.0 Å. Consider a pair of atoms A and B that are 8.1 Å apart when the pairlist is built. If the pair list includes only those atoms within the cutoff distance, this pair would not be included in the list. Now assume that after five timesteps, atoms A and B have moved to only 7.9 Å apart. A and B are now within the cutoff distance of each other, and should have their non-bonded interactions calculated. However, because the non-bonded interactions are based solely on the pair list and the pair list will not be rebuilt for another five timesteps, this pair will be ignored for five timesteps causing energy not to be conserved within the system.

To avoid this problem, the parameter pairlistdist allows the user to specify a distance greater than the cutoff distance for pairs to be included in the pair list, as shown in Figure 4. Pairs that are included in the pair list but are outside the cutoff distance are simply ignored. So in the above example, if the pairlistdist were set to 10.0 Å, then the atom pair A and B would be included in the pair list, even though the pair would initially be ignored because they are further apart than the cutoff distance. As the pair moved closer and entered the cutoff distance, because the pair was already in the pair list, the non-bonded interactions would immediately be calculated and energy conservation would be preserved. The value of pairlistdist should be chosen such that no atom pair moves more than $\text{\texttt{pairlistdist}}-\text{\texttt{cutoff}}$ in one cycle. This will insure energy conservation.