Is an Intuitive Convergence Definition of Molecular Dynamics Simulations Solely Based on the Root Mean Square Deviation Possible?

Root Mean Square Deviation Probability Analysis of Molecular Dynamics Trajectories on DNA

The comparison and detection of the commonalities and differences in multiple structural ensembles is an important step in the use of molecular simulations to gain insight into the conformation and dynamics of complex biomacromolecules. While the average structure is often employed as the representative of an ensemble of structures in such comparisons, dynamic molecular systems with multiple co...

Convergence of Monte Carlo Simulations involving the Mean-Reverting Square Root Process∗

The mean-reverting square root process is a stochastic differential equation (SDE) that has found considerable use as a model for volatility, interest rate, and other financial quantities. The equation has no general, explicit, solution, although its transition density can be characterized. For valuing path-dependent options under this model, it is typically quicker and simpler to simulate the ...

On Weighted Pcm and Mean Square Deviation

How Magnification of the Root-Mean-Square Deviation (RMSD) Value Affects the Convergence Speed of Hopfield Neural Network Classifier

The Root Mean Square-Deviation (RMSD) or Root Mean Square Error (RMSE) is the frequently used measure of the difference between values predicted by a model or an estimator and the values actually observed from that which is being modelled or estimated. In this paper, we show that the magnification of the RMSE, when used with the classifier Hopfield Neural Network (HNN), may help the network to ...

LB3D: A Protein Three-Dimensional Substructure Search Program Based on the Lower Bound of a Root Mean Square Deviation Value

Searching for protein structure-function relationships using three-dimensional (3D) structural coordinates represents a fundamental approach for determining the function of proteins with unknown functions. Since protein structure databases are rapidly growing in size, the development of a fast search method to find similar protein substructures by comparison of protein 3D structures is essentia...