[gmx-users] Re: Diffusion constant

[Vitaly Chaban]

Dear Teobaldo,

I think your calculation should be as easy as:
"
g_msd -n index.ndx
"
where index.ndx contains the atom numbers belonging to that "one
molecule in water".

Good luck,
Vitaly


> Dear Users
> I want to calculate the diffusion constant of one molecule in water.I make this calculation in the followin way:
> Obtaining a continuos trajectory
> 1) trjconv -f traj.trr -pbc nojump -o traj_nojump.xtc
>
> Obtaining the msd of the solute, removing the center of mass of the system
> Firt 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 -mv
> I choose SOLUTE
>
> There are significative differences in the results?
> according to the gromacs manual -mv option is used in molecules,
>
> What is the correct step, 2a or 2b?
>
>
> Regards
> Teobaldo
>