Paper Citing NAMD - Abstract
Makrodimitris, K.; Fernandez, E.J.; Woolf, T.B.; O'Connell, J.P.
ALLD: An object-oriented mesoscopic simulation program for polar biomolecules in hydrophobic chromatography or biomembranes
MOLECULAR SIMULATION, 31:623-636, AUG 2005
The ALLD simulation software implements a mesoscopic lattice method to model hydrophobic chromatographic systems and biomembranes. The basis and some initial results of these applications emphasizing reversed phase chromatography of peptides are reviewed. The program structure and coding are described along with concepts for parallelization to simulate massive systems and large biomolecules. Extensions of the method for simulations with variable temperature, solute and solvent polarization, effects of ionized solutes and added salts and heterogeneous media are presented.
