Hello, I have used GMX select-on to select the region and specify the molecule (see figure) . But when I run MSD, there was an error“The index group does not consist of whole molecules,” so I tried to fix it with GMX trjconv-pbc, but GMX TRJCONV can only output a trace file, not an NDX file. So I would like to ask what should be done. Thank you.
With that selection string you will only select the atoms that are in the chosen region. I would try to find a selection string that is not as strict regarding the region.
Anyhow, what options do you use to your gmx msd command?