[gmx-users] g_msd and Diffusion Constant

[Ganesh Shahane]

Yes, for some calculations the error bar values did exceed the diffusion
coefficient values.

I am using the double-precision version of gromacs. But then again the
question is whether to consider the value displayed on the terminal screen
or the one displayed in the .xvg file.

On Tue, Jul 21, 2015 at 10:25 PM, V.V.Chaban <vvchaban at gmail.com> wrote:

> I have a strong belief that an error bar for such numbers exceed the
> diffusion coefficient values.
>
> Newer gromacs versions (or is it just because of a double-precision
> compilation?) output more digits. I do want to hope these digits are
> meaningful....
>
> If I got this situation, I would report 10^(-8)cm^2/s.
>
>
>
>
>
> On Tue, Jul 21, 2015 at 2:14 AM, Ganesh Shahane
> <ganesh7shahane at gmail.com> wrote:
> > Hi!
> >
> > I am using gromacs version 4.5.5. The values are different. The value
> > displayed on the terminal screen is 0.0007417*1e-5 cm^2/s while the value
> > displayed in the chol.xvg file is 0.000903331*1e-5 cm^2/s.
> >
> > As you can see, both values are quite close though the value in chol.xvg
> > doesn't appear to be round up.
> >
> > On Tue, Jul 21, 2015 at 10:20 AM, Chandan Choudhury <iitdckc at gmail.com>
> > wrote:
> >>
> >> Hi!!
> >>
> >> Are the values different? Can you show us both the values?
> >> I presume both values would be same.
> >> The value in the xvg file would be round up.
> >>
> >> Chandan
> >>
> >>
> >> On Tue, Jul 21, 2015 at 1:33 AM, V.V.Chaban <vvchaban at gmail.com> wrote:
> >>
> >> > which version fo you use?
> >> >
> >> >
> >> >
> >> >
> >> >
> >> > On Mon, Jul 20, 2015 at 8:28 AM, Ganesh Shahane
> >> > <ganesh7shahane at gmail.com> wrote:
> >> > > Dear Gromacs Users,
> >> > >
> >> > > I have performed a simulation of a POPC+Cholesterol bilayer. I wish
> to
> >> > know
> >> > > the diffusion constant of a particular cholesterol molecule. Towards
> >> > this,
> >> > > I performed a g_msd using the command as follows-
> >> > >
> >> > > g_msd -f 30chol.xtc -s prod.tpr -lateral z -endfit 800000 -n
> index.ndx
> >> > -mol
> >> > > chol.xvg
> >> > >
> >> > > where index.ndx contains a single index for the cholesterol atoms in
> >> > > question. In the end, I got 2 different values of diffusion
> constant,
> >> > with
> >> > > one of them being displayed on the terminal screen and the other
> value
> >> > > in
> >> > > the chol.xvg file.
> >> > >
> >> > > Does anyone have any idea as to which value should be taken as the
> >> > > value
> >> > of
> >> > > diffusion constant? Any help would be appreciated. Thank you!
> >> > >
> >> > > --
> >> > > Best Regards,
> >> > > Ganesh Shahane
> >> > > --
> >> > > Gromacs Users mailing list
> >> > >
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> >> > --
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> >>
> >>
> >>
> >> --
> >>
> >> Chandan Kumar Choudhury
> >> National Chemical Laboratory, Pune
> >> India
> >>
> >> *"All work and no play makes Jack a dull boy...”*
> >> --
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> >
> >
> >
> > --
> > Best Regards,
> > Ganesh Shahane
> --
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-- 
Best Regards,
Ganesh Shahane