Dear gromacs users,
I am currently working with polymer and studying the effect on a protein. I am generating the polymer configuration and protein configuration separately. So I am equilibrating the protein and the polymer in water for long time and then extract the polymer configuration and inserting in the protein using gmx insert-molecules by replacing water molecules.
For this purpose I am removing PBC from the final gro file obtained for the protein-in-water equilibration simulation (pbc_protein_water.gro) and removing PBC from the final gro file obtained for the polymer-in-water equilibration simulation and extracting polymer coordinates only (pbc_polymer.gro), making sure there is no broken molecule or outside boundary as that might have an effect while using gmx insert-molecules. Then I am inserting the pbc_polymer.gro into the pbc_protein_water.gro by using the gmx insert-molecules tool by replacing water molecules. Is this fine or we don’t need to remove PBC for preparing the initial configuration for the protein-polymer-water system?
Any suggestion(s) is much appreciated.