Paper Citing NAMD - Abstract
Gorecki, Adam; Szypowski, Marcin; Dlugosz, Maciej; Trylska, Joanna
RedMD-Reduced Molecular Dynamics Package
JOURNAL OF COMPUTATIONAL CHEMISTRY, 30:2364-2373, NOV 15 2009
We developed a software package (RedMD) to perform molecular dynamics simulations and normal mode analysis of reduced models of proteins, nucleic acids, and their complexes. With RedMD one can perform molecular dynamics simulations in a microcanonical ensemble, with Berendsen and Langevin thermostats, and with Brownian dynamics. We provide force field and topology generators which are based on the one-bead per residue/nucleotide elastic network model and its extensions. The user can change the force field parameters with the command line options that are passed to generators. Also. the generators can be modified. for example, to add new potential energy functions. Normal mode analysis tool is available for elastic or anisotropic network models. The program is written in C and C++ languages and the structure/topology of a molecule is based on an XML format. OpenMP technology for shared-memory architectures was used for code parallelization. The code is distributed under GNU public licence and available at http://bionano.icm.edu.pl/software/. (C) 2009 Wiley Periodicals, Inc. J Comput Chem 30: 2364-2373. 2009
