A short guide for molecular dynamics simulations of RNA systems Export

@article{citeulike:4457446, abstract = {As a result of important methodological advances and of the rapid growth of experimental data, the number of molecular dynamics (MD) simulations related to RNA systems has significantly increased. However, such MD simulations are not straightforward and great care has to be exerted during the setup stage in order to choose the appropriate MD package, force fields and ionic conditions. Furthermore, the choice and a correct evaluation of the main characteristics of the starting structure are primordial for the generation of informative and reliable MD trajectories since experimental structures are not void of inaccuracies and errors. The aim of this review is to provide, through numerous examples, practical guidelines for the setup of MD simulations, the choice of ionic conditions and the detection and correction of experimental inaccuracies in order to start MD simulations of nucleic acid systems under the best auspices.}, author = {Hashem, Yaser and Auffinger, Pascal}, citeulike-article-id = {4457446}, citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.ymeth.2008.09.020}, citeulike-linkout-1 = {http://linkinghub.elsevier.com/retrieve/pii/S1046202308001576}, doi = {10.1016/j.ymeth.2008.09.020}, issn = {10462023}, journal = {Methods}, keywords = {rna}, month = {March}, number = {3}, pages = {187--197}, posted-at = {2009-05-04 11:29:20}, priority = {2}, title = {A short guide for molecular dynamics simulations of RNA systems}, url = {http://dx.doi.org/10.1016/j.ymeth.2008.09.020}, volume = {47}, year = {2009} }

TY - JOUR ID - citeulike:4457446 L3 - citeulike-article-id:4457446 N2 - As a result of important methodological advances and of the rapid growth of experimental data, the number of molecular dynamics (MD) simulations related to RNA systems has significantly increased. However, such MD simulations are not straightforward and great care has to be exerted during the setup stage in order to choose the appropriate MD package, force fields and ionic conditions. Furthermore, the choice and a correct evaluation of the main characteristics of the starting structure are primordial for the generation of informative and reliable MD trajectories since experimental structures are not void of inaccuracies and errors. The aim of this review is to provide, through numerous examples, practical guidelines for the setup of MD simulations, the choice of ionic conditions and the detection and correction of experimental inaccuracies in order to start MD simulations of nucleic acid systems under the best auspices. IS - 3 JF - Methods SN - 10462023 EP - 197 TI - A short guide for molecular dynamics simulations of RNA systems VL - 47 SP - 187 KW - rna AU - Hashem, Yaser AU - Auffinger, Pascal PY - 2009/03// UR - http://dx.doi.org/10.1016/j.ymeth.2008.09.020 ER -