How to ensure solvent molecules are contiguous

User discussions
1

GROMACS version: 2023
GROMACS modification: No

I am preparing a system in which I am including structural waters, and also adding waters using solvate. In my starting pdb the structural waters are in a separate chain, which comes last after some polypeptide chains. After solvate, structural waters appear in the coordinate file as HOH, and start after the last polypeptide chain like so:

2517ARG C 4860 5.670 7.760 3.690
2517ARG OT1 4861 5.665 7.859 3.597
2517ARG OT2 4862 5.628 7.769 3.819
1HOH OW 4863 6.689 7.302 2.428
1HOH HW1 4864 6.771 7.302 2.485
1HOH HW2 4865 6.607 7.302 2.485
2HOH OW 4866 6.633 4.500 3.318
2HOH HW1 4867 6.715 4.500 3.376
2HOH HW2 4868 6.633 4.582 3.260

Have a numbering discontinuity that goes back to the original PDB entry:

25HOH OW 4935 4.334 7.236 1.803
25HOH HW1 4936 4.415 7.236 1.860
25HOH HW2 4937 4.252 7.236 1.860
335HOH OW 4938 4.924 7.203 2.470
335HOH HW1 4939 5.006 7.203 2.528
335HOH HW2 4940 4.924 7.284 2.412

And are followed by solvent generated by solvate:

479HOH OW 5364 4.879 6.020 4.914
479HOH HW1 5365 4.879 6.101 4.857
479HOH HW2 5366 4.879 5.938 4.857
480SOL OW 5367 0.230 0.628 0.113
480SOL HW1 5368 0.137 0.626 0.150
480SOL HW2 5369 0.231 0.589 0.021

The topology file has two separate entries for solvent:

[ molecules ]
; Compound #mols
Protein_chain_A 1
Protein_chain_B 1
SOL 168
SOL 8198

After grompp+genion all water molecules are labeled as SOL, are renumbered to continue from the last amino acid:

2517ARG C 4860 5.670 7.760 3.690
2517ARG OT1 4861 5.665 7.859 3.597
2517ARG OT2 4862 5.628 7.769 3.819
2518SOL OW 4863 6.689 7.302 2.428
2518SOL HW1 4864 6.771 7.302 2.485
2518SOL HW2 4865 6.607 7.302 2.485
2519SOL OW 4866 6.633 4.500 3.318
2519SOL HW1 4867 6.715 4.500 3.376
2519SOL HW2 4868 6.633 4.582 3.260

There is no more numbering discontinuity – the solvent waters simply continue counting up until the last molecule added by solvate. However, the topology file still has two separate compound entries for structural and solvate solvent waters, now followed by ions:

[ molecules ]
; Compound #mols
Protein_chain_A 1
Protein_chain_B 1
SOL 168
SOL 8150
NA 19
CL 29

In this case, will all solvent waters be treated as one contiguous block? If not, will changing the two solvent entries in the topology file to:

SOL 8318 ; 8150+168=8318

result in this happening? Will all solvent molecules be treated as one continuous block that requires SETTLE (Solvent.hdb Formatting Inquiry - #9 by jalemkul)? Or is there another source of information for grompp, besides the topology and coordinate files?

2

There is no difference between having one or two blocks with the same moleculetype, except for a minor, unnoticeable performance impact at domain decomposition.