Paper Citing NAMD - Abstract
Dieterich, Johannes M.; Hartke, Bernd
OGOLEM: Global cluster structure optimisation for arbitrary mixtures of flexible molecules. A multiscaling, object-oriented approach
MOLECULAR PHYSICS, 108:279-291, 2010
In practical applications, global cluster structure optimisation has so far been limited largely to homogeneous clusters of atoms or small molecules, with little or no choice in the calculation of inter-particle forces. We eliminate these limitations by presenting a new program suite OGOLEM that is universal by design, both in cluster composition (including arbitrarily heterogeneous clusters of complicated molecules) and in its interfaces to force calculation backends. This is demonstrated by exemplary applications in two novel fields: strongly heterogeneous Lennard-Jones clusters (ternary, quaternary, quinary) and mixed clusters of the aminoglycoside Kanamycin A with sodium cations.
