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

[Arun Srikanth]

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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