How to identify or create correct list from GROMACS options during analysis of trajectory?

User discussions
1

GROMACS version: 2020.4
GROMACS modification: No

How to identify or create correct list from GROMACS options during analysis of trajectory ?

During topology preparation using pdb2gmx Protein_chain_A and Protein_chain_B were identified. However, when production MD was completed and I proceeded to do analysis, I find this list :

Group 0 ( System) has 180960 elements

Group 1 ( Protein) has 12511 elements

Group 2 ( Protein-H) has 6408 elements

Group 3 ( C-alpha) has 791 elements

Group 4 ( Backbone) has 2373 elements

Group 5 ( MainChain) has 3166 elements

Group 6 ( MainChain+Cb) has 3910 elements

Group 7 ( MainChain+H) has 3924 elements

Group 8 ( SideChain) has 8587 elements

Group 9 ( SideChain-H) has 3242 elements

Group 10 ( Prot-Masses) has 12511 elements

Group 11 ( non-Protein) has 168449 elements

Group 12 ( Ion) has 26 elements

Group 13 ( ZN) has 1 elements

Group 14 ( CL) has 1 elements

Group 15 ( NA) has 24 elements

Group 16 ( Water) has 168423 elements

Group 17 ( SOL) has 168423 elements

Group 18 ( non-Water) has 12537 elements

Group 19 ( Water_and_ions) has 168449 elements

There is no mention of Chains A and B. I would like to calculate H-bond between Chain A and Chain B and later do a SMD simulation between these two groups. However, I do not see them in the list.

How to fix this issue ?

2

Use make_ndx to generate index groups corresponding to the different chains.

3

After using pdb2gmx on the cleaned PDB (only removed crystallographic waters), chain A has “resnr” from 19-615 and chain B has “resnr” from 333-526.

When I use make_ndx, how will it differentiate , as the numbers 333-526 are included in the IDs for the first chain as well. The total number of atoms for group protein does not equal to the two groups when I use make_ndx to create two separate groups by using “resnr”

As in the question group Protein has 12511 elements

This is what I observe upon using make_ndx :

r 19-615
Found 12511 atoms with res.nr. in range 19-615
15 r_19-615 : 12511 atoms
r 333-526
Found 6116 atoms with res.nr. in range 333-526
16 r_333-526 : 6116 atoms

Link to GRO file