[gmx-users] Diffusion constant

[David van der Spoel]

On 04/07/16 16:20, pari lotfi wrote:
> Dear Justin,
>
> my C++ code is correct, but diffusion constant of my code and Gromacs are
> not same.
> Perhaps coordinates make this problem.
> coordinates of atoms in the different frames gathered by "g_traj". Is this
> true? Some of the coordinates are out of the box! negative or larger than
> box size.
>
> Thanks for your help,
> Pari
>
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>
You can not expect gromacs users to compare your program to gromacs 
programs. For all I know gms msd works fine, so there probably is some 
misunderstanding. Yes coordinates go out of the box due to periodic 
boundary conditions. Check trjconv options.
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> *> 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? >*
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> * 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
> <https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2010-July/052512.html>*
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> * Then read the gmx msd code and compare it to the code you wrote.*
> * -Justin*
>


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se