GROMACS version: 2023
GROMACS modification: No
I would like to retain some waters from the solved structure I am using to set up my simulation and combine them with solvent waters added by solvate. As Justin pointed out to me here, doing this naively is likely to create discontinuous blocks of water molecules requiring SETTLE. Are there any suggestions for doing this seamlessly to avoid this kind of problem – perhaps by reordering / renumbering water residues in the original pdb so that waters subsequently added by solvate form a continuous block with the structural waters?