Help centering, fitting, and analysis on a protein that contains a chain of D-residues

GROMACS version: 2024.1
GROMACS modification: No

Is there a way to have gmx trjconv center on multiple groups at once? My simulated protein has both L and D residues in the main chain. However, the choices I’m offered split the protein into the L residue component (Group 1), and each D residue as an individual component (Groups 13 - 18).

Or is there a way to have gromacs read my .tpr file and recognize that the L and D residue components should be counted as one group?

[samdintd@cn4270 concatonate]$ gmx trjconv -s md_66_0_50.tpr -f md_66_0_300.xtc -o md_66_0_300_reimage_test.xtc -pbc mol -ur compact -center
:-) GROMACS - gmx trjconv, 2024.4 (-:

Executable: /usr/local/apps/gromacs/2024.4-intel2022/bin/gmx
Data prefix: /usr/local/apps/gromacs/2024.4-intel2022
Working dir: /gpfs/gsfs12/users/samdintd/gromacs/Ripple/strand_4/output_S4_16_0066/concatonate
Command line:
gmx trjconv -s md_66_0_50.tpr -f md_66_0_300.xtc -o md_66_0_300_reimage_test.xtc -pbc mol -ur compact -center

Note that major changes are planned in future for trjconv, to improve usability and utility.
Will write xtc: Compressed trajectory (portable xdr format): xtc
Reading file md_66_0_50.tpr, VERSION 2024.1 (single precision)
Reading file md_66_0_50.tpr, VERSION 2024.1 (single precision)
Select group for centering
Group 0 ( System) has 13758 elements
Group 1 ( Protein) has 784 elements
Group 2 ( Protein-H) has 383 elements
Group 3 ( C-alpha) has 50 elements
Group 4 ( Backbone) has 150 elements
Group 5 ( MainChain) has 200 elements
Group 6 ( MainChain+Cb) has 246 elements
Group 7 ( MainChain+H) has 251 elements
Group 8 ( SideChain) has 533 elements
Group 9 ( SideChain-H) has 183 elements
Group 10 ( Prot-Masses) has 784 elements
Group 11 ( non-Protein) has 12974 elements
Group 12 ( Other) has 107 elements
Group 13 ( DPHE) has 20 elements
Group 14 ( DGLU) has 15 elements
Group 15 ( DILE) has 19 elements
Group 16 ( DASN) has 14 elements
Group 17 ( DLEU) has 19 elements
Group 18 ( DSER) has 12 elements
Group 19 ( NA) has 9 elements
Group 20 ( CLA) has 8 elements
Group 21 ( Water) has 12858 elements
Group 22 ( SOL) has 12858 elements
Group 23 ( non-Water) has 900 elements
Group 24 ( Ion) has 9 elements
Group 25 ( Water_and_ions) has 12867 elements

What do you mean precisely with center on multiple groups?

If the group you want to center is not available in the standard index file or in the .tpr you are using, you can generate a new index file with gmx make_ndx that contains the group with respect to which you plan to center, and then pass this new index file to gmx trjconv.