[gmx-users] RE: Diffusion constant

[Justin A. Lemkul]

Ricardo Cuya Guizado 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?
> 
> 

No, your two commands are identical.  The -mw option is set to "yes" by default, 
so in essence, 2a actually uses -mw as well.  The -mol option plots MSD per 
molecule, perhaps that's what you're referring to?

-Justin

> 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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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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