[gmx-users] Diffusion constant

[Justin Lemkul]

On 7/1/16 6:33 PM, pari lotfi wrote:
> Dear all,
>
> I saw in the different simulation that the number of restart point affect
> on the D! What is the rule of restart point on the diffusion constant
> calculation?
> **"The diffusion constant is calculated by least squares fitting a straight
> line"**
>
> Then all the "msd" doesn't rule in fitting and D?
>
> If yes, how do I select least squares?
>
> **"note that t is time from the reference positions, not simulation time" **
>
> What is reference position? Are the reference point and restart point is
> the same? How can I fit on references position instead simulation time?
>

This is the most complete explanation of the algorithm I've seen yet:

https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2010-July/052512.html

Then read the gmx msd code and compare it to the code you wrote.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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