[gmx-users] Re: Diffusion constant

[Vitaly Chaban]

Ricardo,

"-mol" is for each molecule separately. So averaging among (identical)
molecules will not be performed. As I suppose this is for the
different debug runs mostly. To get the ordinary diffusion constant
just
"
g_msd
"
is enough. To get the diffusion constant of any specific group of
atoms, use NDX file and type the atom numbers there.

Good luck,
Vitaly


On Mon, Jun 28, 2010 at 8:22 PM, Ricardo Cuya Guizado
<rcuyag at hotmail.com> wrote:
> Dears Justin and Vitaly
>
> I make a mistake in my firts e-mail
>
> the option is not -mv is -mol as Justin mentioned
>
> So the second step was:
>
> Obtaining the msd of the solute, removing the center of mass of the
> system
>
> Firts way:
> 2a) g_msd -f traj_nojump.xtc -s topol.tpr -n index.ndx -o
> msd_solute.xvg -rmcomm
> I choose SOLUTE
> Second way
>  2b) g_msd -f traj_nojump.xtc -s topol.tpr -n index.ndx -rmcomm
> -o msd_solute.xvg -rmcomm -mol
>  I choose SOLUTE
>
>  In the two cases the solute was choose , the differences in the solute
> Cont. Diffusion is in one order of magnitude.
>  What is the correct step for calculate the Dif. const , 2a or 2b?
>
> Regars
>
> Ricardo
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