To further reduce the cost of computing full electrostatics,
NAMD uses a multiple time stepping integration scheme. In this scheme,
the total force acting on each atom is broken into two pieces, a local
component and a long range component.
The local force component is defined in terms of a
local interaction distance.
The local force component consists of all bonded interactions
as well as all non-bonded interactions for pairs that are separated by
less than the local interaction distance.
The long range component consists only of
electrostatic interactions outside of the local interaction distance.
Since the long range forces are slowly varying, they are not evaluated
every timestep. Instead, they are evaluated every k timesteps,
where each set of k timesteps is referred to as a cycle.
The value of k is specified by the NAMD parameter
stepspercycle.
There are several ways in which the long range forces
may be combined with the short range forces.
See section 5.2.1
for an explanation of the various multiple time stepping
options available.
For appropriate values of k,
it is believed that the error introduced by this infrequent evaluation
of the long range forces
is modest compared to the error already incurred by the use of the numerical
(Verlet) integrator.
The performance of NAMD with the use of DPMTA to provide
full electrostatics approximately doubles the
run time of a simulation as compared to NAMD with an
8.0 Å electrostatic cutoff.
Improved methods for incorporating these long range forces
are currently being investigated,
with the intention of improving accuracy as well as
reducing the frequency of long range force evaluations.
In the scheme described above, the van der Waals forces are still
truncated at the local interaction distance.
Thus, the van der Waals cutoff distance
forms a lower limit to the local interaction distance. While this is
believed to be sufficient, there are investigations underway to remove
this limitation and provide full van der Waals calculations in
time as well.