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

[Kevin Boyd]

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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