RedMD - Reduced molecular dynamics package Export

@article{citeulike:4117949, abstract = {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 . {\copyright} 2009 Wiley Periodicals, Inc. J Comput Chem, 2009}, address = {Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw, 02-106 Warsaw, Poland; Department of Biophysics, Faculty of Physics, University of Warsaw, 02-089 Warsaw, Poland}, author = {G\'{o}recki, Adam and Szypowski, Marcin and D\ługosz, Maciej and Trylska, Joanna}, citeulike-article-id = {4117949}, citeulike-linkout-0 = {http://dx.doi.org/10.1002/jcc.21223}, citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/19247989}, citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=19247989}, citeulike-linkout-3 = {http://www3.interscience.wiley.com/cgi-bin/abstract/122218930/ABSTRACT}, doi = {10.1002/jcc.21223}, issn = {1096-987X}, journal = {Journal of Computational Chemistry}, keywords = {molecular\_dynamics, programmi}, number = {14}, pages = {2364--2373}, posted-at = {2009-09-15 22:51:51}, priority = {2}, title = {RedMD - Reduced molecular dynamics package}, url = {http://dx.doi.org/10.1002/jcc.21223}, volume = {30}, year = {2009} }

TY - JOUR ID - citeulike:4117949 L3 - citeulike-article-id:4117949 N2 - 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 . © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009 IS - 14 JF - Journal of Computational Chemistry SN - 1096-987X AD - Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw, 02-106 Warsaw, Poland; Department of Biophysics, Faculty of Physics, University of Warsaw, 02-089 Warsaw, Poland EP - 2373 TI - RedMD - Reduced molecular dynamics package VL - 30 SP - 2364 KW - molecular_dynamics KW - programmi AU - Górecki, Adam AU - Szypowski, Marcin AU - Długosz, Maciej AU - Trylska, Joanna PY - 2009/// UR - http://dx.doi.org/10.1002/jcc.21223 ER -