[gmx-users] g_msd and Diffusion Constant

[Chandan Choudhury]

Hi!!

Are the values different? Can you show us both the values?
I presume both values would be same.
The value in the xvg file would be round up.

Chandan


On Tue, Jul 21, 2015 at 1:33 AM, V.V.Chaban <vvchaban at gmail.com> wrote:

> which version fo you use?
>
>
>
>
>
> On Mon, Jul 20, 2015 at 8:28 AM, Ganesh Shahane
> <ganesh7shahane at gmail.com> wrote:
> > Dear Gromacs Users,
> >
> > I have performed a simulation of a POPC+Cholesterol bilayer. I wish to
> know
> > the diffusion constant of a particular cholesterol molecule. Towards
> this,
> > I performed a g_msd using the command as follows-
> >
> > g_msd -f 30chol.xtc -s prod.tpr -lateral z -endfit 800000 -n index.ndx
> -mol
> > chol.xvg
> >
> > where index.ndx contains a single index for the cholesterol atoms in
> > question. In the end, I got 2 different values of diffusion constant,
> with
> > one of them being displayed on the terminal screen and the other value in
> > the chol.xvg file.
> >
> > Does anyone have any idea as to which value should be taken as the value
> of
> > diffusion constant? Any help would be appreciated. Thank you!
> >
> > --
> > Best Regards,
> > Ganesh Shahane
> > --
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-- 

Chandan Kumar Choudhury
National Chemical Laboratory, Pune
India

*"All work and no play makes Jack a dull boy...”*