Estimation of error in the diffusion coefficient from molecular dynamics simulations

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