[gmx-users] RE: Diffusion constant

[Ricardo Cuya Guizado]

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: vvchaban at gmail.com
> To: gmx-users at gromacs.org
> CC: rcuyag at 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
> >
 		 	   		  
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