GROMACS version: 2025.4-conda_forge
GROMACS modification: No
Hello, I am a beginner to GROMACS. I am working on a complex system consisting of protein, DNA and zinc metal ions. I have a 50 ns test trajectory and intend to examine the RMSD variation of this system during the simulation. I have already created an index file for the protein-DNA-zinc ion complex.
However, I am confused about which groups to select for least-squares fitting and RMSD calculation when performing separate RMSD analyses on the protein, DNA, and this custom index group respectively.
- For proteins, most tutorials recommend performing fitting and RMSD calculation on the backbone, which corresponds to group 4, 4, is that correct?
- For DNA, should I pick group 13, 13?
- And for the entire complex, is group 21, 21 the right choice?
I have no confusion regarding the group used for RMSD calculation output, yet I am unsure about the group for least-squares fitting. I have read numerous forum posts and tutorials indicating that the fitting group does not always have to be identical to the group chosen for RMSD computation.
Below is my group information:
Group 0 ( System) has 1383063 elements
Group 1 ( Protein) has 4799 elements
Group 2 ( Protein-H) has 2465 elements
Group 3 ( C-alpha) has 306 elements
Group 4 ( Backbone) has 918 elements
Group 5 ( MainChain) has 1223 elements
Group 6 ( MainChain+Cb) has 1506 elements
Group 7 ( MainChain+H) has 1519 elements
Group 8 ( SideChain) has 3280 elements
Group 9 ( SideChain-H) has 1242 elements
Group 10 ( Prot-Masses) has 4799 elements
Group 11 ( non-Protein) has 1378264 elements
Group 12 ( Ion) has 2691 elements
Group 13 ( DNA) has 4762 elements
Group 14 ( ZN) has 9 elements
Group 15 ( NA) has 1407 elements
Group 16 ( CL) has 1275 elements
Group 17 ( Water) has 1370811 elements
Group 18 ( SOL) has 1370811 elements
Group 19 ( non-Water) has 12252 elements
Group 20 ( Water_and_ions) has 1373502 elements
Group 21 ( protein_DNA_zn) has 9570 elements