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 <[email protected]> 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 > ________________________________ > Courez la chance de voir la photo de votre coin de pays sur Bing.ca > Soumettez une photo maintenant! -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
