nMoldyn 3: using task farming for a parallel spectroscopy-oriented analysis of molecular dynamics simulations.
We present a new version of the program package nMoldyn, which has been originally developed for a neutron-scattering oriented analysis of molecular dynamics simulations of macromolecular systems (Kneller et al., Comput. Phys. Commun. 1995, 91, 191) and was later rewritten to include in-depth time series analyses and a graphical user interface (Rog et al., J. Comput. Chem. 2003, 24, 657). The main improvement in this new version and the focus of this article are the parallelization of all the analysis algorithms for use on multicore desktop computers as well as distributed-memory computing clusters. The parallelization is based on a task farming approach which maintains a simple program structure permitting easy modification and extension of the code to integrate new analysis methods.
Centre de Biophysique Moléculaire (CNRS), Rue Charles Sadron, 45071 Orléans, France.
Konrad
K
Hinsen
Eric
E
Pellegrini
Sławomir
S
Stachura
Gerald R
GR
Kneller
D000465:Algorithms; D056004:Molecular Dynamics Simulation; D013057:Spectrum Analysis