[gmx-users] g_msd and Diffusion Constant

[Ganesh Shahane]

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
> > >
> > > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
>
>
>
> --
>
> Chandan Kumar Choudhury
> National Chemical Laboratory, Pune
> India
>
> *"All work and no play makes Jack a dull boy...”*
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>



-- 
Best Regards,
Ganesh Shahane