GROMACS version: 2021.3
GROMACS modification: No
I am trying to strip solvent from the MD trajectory. The command
gmx trjconv -s npt_prod.tpr -f npt_prod.xtc -n index.ndx -pbc nojump -o npt_prod_nowat_nojump.xtc
works as expected, selecting the option for the zinc ion and the protein, but
gmx convert-tpr -s npt_prod.tpr -n index.ndx -nsteps -1 -o npt_prod_nowat_nojump.tpr
does not work, giving the error “Cannot do both runtime modification and charge-zeroing/index group extraction in a single call.”
I do not understand this error, could anyone provide some help as to how to address this. Or is there a better way of stripping water molecules from the MD trajectory?