Mean squared displacement - Wikipedia
In statistical mechanics, the mean squared displacement (MSD, also mean square displacement, average squared displacement, or mean square fluctuation) is a measure of the deviation of the position of a particle with respect to a reference position over time.
如何理解“均方位移MSD”这个概念？ - 知乎
定义：均方位移（Mean Square Displacement, MSD），指的是粒子随时间移动后的位置相对于参考位置的偏差的量度。 当观测时间趋于无穷大时，MSD与极限观测时间成正比。
4.8.2.2. Mean Squared Displacement — MDAnalysis.analysis.msd ...
MSDs can be used to characterize the speed at which particles move and has its roots in the study of Brownian motion. For a full explanation of the theory behind MSDs and the subsequent calculation of self-diffusivities the reader is directed to 1. MSDs can be computed from the following expression, known as the Einstein formula:
Identifying short- and long-time modes of the mean-square …
2019年5月16日 · In this work, we present a new optimal and robust nonlinear regression model capable of fitting the MSD function with different regimes corresponding to different time scales. The algorithm presented here achieves two major goals; a more accurate estimation of D as well as extracting information about the short time behavior.
4.7.2.2. Mean Squared Displacement — MDAnalysis.analysis.msd ...
MSDs can be used to characterize the speed at which particles move and has its roots in the study of Brownian motion. For a full explanation of the theory behind MSDs and the subsequent calculation of self-diffusivities the reader is directed to [Maginn2019]. MSDs can be computed from the following expression, known as the Einstein formula:
MD2D: A python module for accurate determination of diffusion ...
2023年3月1日 · We implemented the algorithm that calculates and corrects the diffusion coefficient as a function of time interval in a python module named MD2D. MD2D calculates the MSD, self-diffusion coefficient, stress auto-correlation function, the bulk and shear viscosities, and provides plots of the calculated quantities.
gmx msd - GROMACS 2024.4 documentation
gmx msd computes the mean square displacement (MSD) of atoms from a set of initial positions. This provides an easy way to compute the diffusion constant using the Einstein relation. The time between the reference points for the MSD calculation is set with -trestart.
8.3.8. Calculate diffusion coefficients — LAMMPS documentation
The first method is to measure the mean-squared displacement (MSD) of the system, via the compute msd command. The slope of the MSD versus time is proportional to the diffusion coefficient.
Mean Square Displacement - GROMACS 2024.4 documentation
To determine the self diffusion coefficient D A of particles of type A, one can use the Einstein relation 108: (458) lim t → ∞ ‖ r i (t) − r i (0) ‖ 2 i ∈ A = 6 D A t. This mean square displacement and D A are calculated by the program gmx msd. Normally an index file containing atom numbers is used and the MSD is averaged over these atoms.
Guidelines for the Fitting of Anomalous Diffusion Mean Square
2015年2月13日 · We extract the precision and accuracy of the fitted MSD for various anomalous exponents and measurement errors with respect to measurement length and maximum time lags. Based on the calculated precision maps, we present …
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