[gmx-users] Question about Mean Square Displacement (MSD)

[Sina Omrani]

Thanks, Kevin,
I am looking for the MSD vs lag plot. I use the saved frames that specified
in mdp file. Is that the problem? I saved positions every 10 ps for a 6000
ps simulation. should I lower this or is there another way for using more
trajectories?

On Sun, 19 Apr 2020 at 00:10, Kevin Boyd <kevin.boyd at uconn.edu> wrote:

> Hi,
>
> Are you talking about the reported diffusion coefficient or the MSD vs lag
> plot? You should be very careful about where you fit. By default, Gromacs
> calculates MSDs at much longer lag times than you typically have good data
> for. Use the -beginfit and -endfit options to restrict the fit to the lag
> times where the MSD plot is linear.
>
> >    I use trjconv command and use the output .gro file
>
> This doesn't make much sense, how many frames are you analyzing?
>
>
> On Sat, Apr 18, 2020 at 12:00 PM Arun Srikanth <askforarun at gmail.com>
> wrote:
>
> > *Message sent from a system outside of UConn.*
> >
> >
> > Unless you give you give details how you calculate the MSD it will not be
> > possible to help.
> > Are you using unwrapped co-ordinates in your calculations for MSD?
> >
> > Arun
> >
> > On Sat, Apr 18, 2020 at 7:33 PM Sina Omrani <sinaomrani96 at gmail.com>
> > wrote:
> >
> > > Hi,
> > > I am trying to post-processing my results and calculate MSD (mean
> square
> > > displacement) but my answer is different from the MSD value that
> GROMACS
> > > calculated. I use trjconv command and use the output .gro file. I tried
> > to
> > > understand the GROMACS code but I am not a good programmer. Is there
> any
> > > specific detail except the Einstein relation in the manual?
> > >
> > > sorry if here is not the right place to ask this question.
> > > Best regards.
> > >
> > > Sina Omrani.
> > > --
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