[gmx-users] cant compute msd

[Devargya Chakraborty]

After removing the -mol command it worked fine.

On Wed, Jan 8, 2020, 3:53 PM Christian Blau <blau at kth.se> wrote:

> Hi Devargya,
>
>
> I believe it's the mixture of -mol and -o options at the same time that
> leads to the unexpected behaviour - there can
> only be one .xvg output for this tool and we'll see to having it fixed.
>
> Do you get any diff_mol.xvg files instead?
>
>
> The documentation states that
>
> "If -mol is set, gmx msd plots the MSD for individual molecules (including
> making molecules whole across periodic boundaries): for each individual
> molecule a diffusion constant is computed for its center of mass. The
> chosen
> index group will be split into molecules."
>
>
> Best,
>
> Christian
>
>
> On 2020-01-08 11:12, Devargya Chakraborty wrote:
> > hi, when i am using the command
> >   gmx msd -f prd.xtc -n il.ndx -s out3.tpr -mol -o msd.xvg
> >
> > after that choosing a group the following line is coming.
> > Select a group to calculate mean squared displacement for:
> > Group     0 (         System) has  5616 elements
> > Group     1 (          Other) has  5616 elements
> > Group     2 (             c2) has  2376 elements
> > Group     3 (           ntf2) has  3240 elements
> > Group     4 (              N) has   216 elements
> > Group     5 (              N) has   216 elements
> > Select a group: 3
> > Selected 3: 'ntf2'
> > Split group of 3240 atoms into 216 molecules
> > Reading frame    5000 time 20000.000   Killed
> >
> > and i cant get the msd file any suggestion regarding this??
> >
> > thank you
> --
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