[gmx-users] Re: Diffusion constant

[Vitaly Chaban]

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
<rcuyag at 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: 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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