For comparison to Dt from experiment, there are two major additional factors: a finite size correction (1), and for many water models, a viscosity correction. We've done both for disaccharides in TIP3P water recently (2).
(1) Yeh, I. C.; Hummer, G. J. Phys. Chem. B 2004, 108, 15873–15879.
(2) Venable, R.M.; Hatcher, E.; Guvench, O.; Alexander D. MacKerell, A.D. Jr.; and Pastor, R.W. J. Phys. Chem. B 2010, 114, 12501-12507.
An additional note-- one cannot use COOR ANAL for this; you must first use MERGE COOR UNFOLD, then get the center-of-mass time series for each molecule via the ATOM time series type in CORREL, followed by CORFUN with the DIFF keyword.
Last edited by rmv; 10/15/10 05:33 PM. Reason: full citation for ref (2)