gmx msd cannot output two xvg files as suggested by command line option
#request to fix msd xvg output behaviour
When using -mol and -o in gmx msd simulatneously, only the xvg files related to the -mol option are output and not the file related to the -o option.
We should either warn about the clashing command line options, or enable output of both.
Here is the original related user mail
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