gmx solvate should work with molecules
gmx solvate can not handle molecules as solvent. According to the documentation it uses the residue number in the input file, ("In practice
this means that two subsequent solvent molecules in the solvent coordinate
file should have different residue number.") but this is not entirely correct since the residue names are interpreted as well. As a results a molecule containing more than one residue with different names (even if they have the same residue number) is torn apart by gmx solvate.
The obvious solution would be to use real the molecule information in a tpr file.
#1 Updated by Teemu Murtola about 3 years ago
It interprets residues exactly like every other Gromacs program, but the help text hasn't been updated to match the new implementation that also considers residue names.
A workflow that would require a tpr file as solvent would not be particularly practical, either.
#3 Updated by Teemu Murtola about 3 years ago
Note that is we want to really use gmx_mtop_t everywhere, the whole tool and the helpers it uses needs to be rewritten to not use t_atoms, and that will also probably solve this. Doing something else is likely to waste significant effort (since you would need to make the helpers aware of molecules, in a way that is not compatible with gmx_mtop_t).