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

[Sina Omrani]

I use a file that contains the position of each atom at every saved frame.
For the first time lag, I distract all trajectories that are 1 timestep
different and averaging the result and so on. I tried the various methods
with different systems but none of them worked.

PS: here is the .gro file. I hope the link works.
https://gofile.io/?c=meQ1dJ

On Sat, 18 Apr 2020 at 23:30, Arun Srikanth <askforarun at gmail.com> wrote:

> 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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