[gmx-users] Use all-atom PDB or coarse-grained PDB as the restraints for grompp a coarse-grained gro?

[ZHANG Cheng]

In Gromacs 2018, -r is used to provide the restraint file for grompp.


I have a grompp command used for a coarse-grained (CG) gro file, i.e. CG.gro:


gmx grompp -f parameter.mdp -r AllAtom.pdb/CG.pdb -c CG.gro -p system.top -o MD.tpr


So in the command above, should I use AllAtom.pdb or CG.pdb as the file for "-r"?


I tried both, and both can work without errors.


But which one is more logically correct?


I think the CG.pdb should definitely work. But why AllAtom.pdb is still okay?