Estimation of error in the diffusion coefficient from molecular dynamics simulations

Chitra, R and Yashonath, S (1997) Estimation of error in the diffusion coefficient from molecular dynamics simulations. In: Journal of Physical Chemistry B, 101 (27). pp. 5437-5445.

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Abstract

Long molecular dynamics simulations (120 ns) of guests confined in zeolite NaCaA as well as that of pure fluid have been carried out in the microcanonical ensemble to obtain an estimate of the error associated with the diffusion coefficient (D). It is found that the error is about 50% for a 1 ns run for argon parameters in NaCaA zeolite. It is found that shorter runs lead to an overestimation of the value of D. It is also found that a linear fit to a region of the msd (mean squared displacement) below similar to 200 ps leads to an overestimation of D. For runs that are sufficiently long, the initial configuration has no effect on D. Further, the values obtained from the msd and the velocity autocorrelation function converge for the runs reported here. It is shown that the error in D depends on the nature of the system and its underlying potential energy surface. The calculated statistical inefficiency suggests that the averages of properties such as the total energy will be uncorrelated over blocks longer than 150 ps. Dependence of the error in D on the simulation length and size is reported.

Item Type:	Journal Article
Publication:	Journal of Physical Chemistry B
Publisher:	American Chemical Society
Additional Information:	Copyright of this article belongs to American Chemical Society.
Department/Centre:	Division of Interdisciplinary Sciences > Supercomputer Education & Research Centre Division of Chemical Sciences > Solid State & Structural Chemistry Unit
Date Deposited:	17 Jul 2009 09:08
Last Modified:	19 Sep 2010 05:26
URI:	http://eprints.iisc.ac.in/id/eprint/18953

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