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#25534 10/05/10 10:19 AM
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Dear All,

I'm hoping someone can answer this problem.

I'm busy calculating the translational diffusion coefficients of several solutes using MSD. Having obtained the MSD I have to fit a straight line and obtain the gradient, from which the diffusion coefficient is calculated.

In the fitting of the straight line, do I make the fit through the initial collision region of the MSD or do I ignore this region and only fit from the steady state region?

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Rich

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Ignore the inertial region in the beginning.


Lennart Nilsson
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Dear Prof.

Thank you for the quick response.

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Rich

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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)

Rick Venable
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For a rectangular box I believe COOR ANAL handles PBC for the MSD calculation. Shouldn't COOR ANAL work on UNFOlded trajectories?


Lennart Nilsson
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COOR ANAL does not seem to provide a means of getting the center-of-mass (COM) motion for larger, more flexible molecules. It appears to be limited to small, rigid solvent molecules, where a single atom is a useful surrogate for the COM, so it's okay for water and ions. However, I could not get reasonable results (identical to rigorous COM results) for neat heptane and pentadecane using COOR ANAL.


Rick Venable
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Yes, this could be a problem; if this is a common type of analysis, and the use of a single atom as a surrogate for the COM is really bad we should add the COM option to COOR ANAL (and extend its PBC awareness).


Lennart Nilsson
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Dear Prof Nilson and Dr Venable

Thank you both for your comments. I will look at these and the references before continuing with my Dt calculations.

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Rich

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An additional note-- in order to apply the finite size correction of Yeh & Hummer, the simulation viscosity is required, a non-trivial task. Changes to c35b1 and later versions have made that somewhat easier; in brief, the pressure tensor from every integration is required, from either fairly long or replicate NVT simulations. The correction becomes small for larger systems, such as a cube of over 100 A edge, but I don't know the size where it becomes negligible.

Contact me via email if you are interested in a copy of ref (2) above, or copies of the scripts I used.


Rick Venable
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Dear Dr Venable,

Thank you for the additional note. Please can you inform me on where to obtain your email address to enquire about the input scripts.

Regards
Rich

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