Sampling Performance of Multiple Independent Molecular Dynamics Simulations of an RNA Aptamer
Shuting Yan, Jason M. Peck, Müslüm İlgü, Marit Nilsen‐Hamilton, Monica H. Lamm
Abstract
predicted structures is a promising approach to achieve sufficient sampling. This approach avoids undesirable outcomes, such as the problem of the RNA aptamer being trapped in a local minimum. For others wishing to conduct multiple independent simulations, the analysis protocol presented in this study is a guide for examining overall sampling and determining if more simulations are necessary for sufficient sampling.
Topics & Concepts
Molecular dynamicsAptamerSampling (signal processing)RNABiological systemUmbrella samplingChemistryStatistical physicsEnergy landscapeMonte Carlo methodComputational chemistryPhysicsMathematicsStatisticsBiologyOpticsGeneGeneticsBiochemistryDetectorRNA and protein synthesis mechanismsProtein Structure and DynamicsMass Spectrometry Techniques and Applications