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