Paper Citing NAMD - Abstract
Berti, Claudio; Furini, Simone; Gillespie, Dirk
PACO: PArticle COunting Method To Enforce Concentrations in Dynamic Simulations
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 12:925-929, MAR 2016
We present PACO, a computationally efficient method for concentration boundary conditions in nonequilibrium particle simulations. Because it requires only particle counting, its computational effort is significantly smaller than other methods. PACO enables Brownian dynamics simulations of micromolar electrolytes (3 orders of magnitude lower than previously simulated). PACO for Brownian dynamics is integrated in the BROWNIES package (www.phys.rush.edu/BROWNIES). We also introduce a molecular dynamics PACO implementation that allows for very accurate control of concentration gradients.
