[gmx-users] cant compute msd

[Christian Blau]

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