[gmx-users] g_msd and Diffusion Constant

[Ganesh Shahane]

Hi,

Actually you are right. The chol.xvg file shows a value of 0.000903331 and
NOT 0.000903331*1e-5. I initially thought that the .xvg file purposely
doesn't show the "1e-5" value.

But still 0.000903331 is different from 0.0007417 which is displayed on the
terminal screen.

On Tue, Jul 21, 2015 at 11:18 AM, Chandan Choudhury <iitdckc at gmail.com>
wrote:

> Yeah.
>
> Generally, what my observation says that in xvg file you have the round up
> value which has 4 decimal digits.
> But for your one it has 10 decimal degits.
>
> Can you please try with a higher version- 4.6.x?
>
> On Tue, Jul 21, 2015 at 10:44 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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> > >
> > >
> > >
> > > --
> > >
> > > 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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>
>
>
> --
>
> Chandan Kumar Choudhury
> National Chemical Laboratory, Pune
> India
>
> *"All work and no play makes Jack a dull boy...”*
> --
> Gromacs Users mailing list
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-- 
Best Regards,
Ganesh Shahane