# How to ensure solvent molecules are contiguous **URL:** \ **Category:** User discussions\ **Created:** [May 3, 2023, 2:44am UTC](https://gromacs.bioexcel.eu/t/how-to-ensure-solvent-molecules-are-contiguous/6326 "2023-05-03T02:44:50Z")\ **Posts on this page:** 2\ **Page:** 1
**Author:** ![RomanS](https://avatars.discourse-cdn.com/v4/letter/r/5e9695/32.png) [@RomanS](https://gromacs.bioexcel.eu/u/RomanS)\ **Post date:** [May 3, 2023, 2:44am UTC](https://gromacs.bioexcel.eu/t/how-to-ensure-solvent-molecules-are-contiguous/6326/1 "2023-05-03T02:44:51Z")
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](https://gromacs.bioexcel.eu/t/solvent-hdb-formatting-inquiry/5519/9))? Or is there another source of information for `grompp`, besides the topology and coordinate files? ---
**Author:** ![hess](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/hess/32/416_2.png) [@hess](https://gromacs.bioexcel.eu/u/hess)\ **Post date:** [May 3, 2023, 11:44am UTC](https://gromacs.bioexcel.eu/t/how-to-ensure-solvent-molecules-are-contiguous/6326/2 "2023-05-03T11:44:05Z")
There is no difference between having one or two blocks with the same moleculetype, except for a minor, unnoticeable performance impact at domain decomposition.