[gmx-users] Diffusion constant

[pari lotfi]

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


















*> 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
<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*