Ricardo, Hmm... My g_msd (4.0.7) doesn't not have "-mv" option. Do you mean mass-weighted (MW) constant here?
If you want to get the "classical diffusion constant", it is mass-weighted by definition. Vitaly On Mon, Jun 28, 2010 at 4:18 PM, Ricardo Cuya Guizado <rcu...@hotmail.com> wrote: > Dear Vitaly > > > Your answer is equivalente to the 2a option of my firts e-mail. > > > Will you explain me the meaning of the -mv option.?, why not use -mv in my > command line? > There are bit differences between the 2a and 2b option, whic is the correct? > > Regards > > Ricardo > .................................................................................................. >> Date > : Mon, 28 Jun 2010 13:26:33 +0300 >> Subject: Re: Diffusion constant >> From: vvcha...@gmail.com >> To: gmx-users@gromacs.org >> CC: rcu...@hotmail.com >> >> 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 >> > > > ________________________________ > Jeux Messenger : mettez vos amis au défi! Jeux Messenger! -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php