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: [email protected]
> To: [email protected]
> CC: [email protected]
>
> 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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