Paper Citing NAMD - Abstract
Skeel, R.D.; Izaguirre, J.A.
An impulse integrator for Langevin dynamics
MOLECULAR PHYSICS, 100:3885-3891, DEC 20 2002
The best simple method for Newtonian molecular dynamics is indisputably the leapfrog Stormer-Verlet method. The appropriate generalization to simple Langevin dynamics is unclear. An analysis is presented comparing an 'impulse method' (kick; fluctuate; kick), the 1982 method of van Gunsteren and Berendsen, and the Brunger-Brooks-Karplus (BBK) method. It is shown how the impulse method and the van Gunsteren-Berendsen methods can be implemented as efficiently as the BBK method. Other considerations suggest that the impulse method is the best basic method for simple Langevin dynamics, with the van Gunsteren-Berendsen method a close contender.
