[gmx-users] Re: Diffusion constant

Vitaly Chaban vvchaban at gmail.com
Mon Jun 28 19:49:52 CEST 2010


"-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
is enough. To get the diffusion constant of any specific group of
atoms, use NDX file and type the atom numbers there.

Good luck,

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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