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
> >
_________________________________________________________________
Regardez-moi dans les yeux : vidéobavardage GRATUIT
http://go.microsoft.com/?linkid=9734396--
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
