GROMACS version:2021
GROMACS modification: Yes/No
How to apply positional restrain for specific residues in the protein that those coordinates remain fixed when Production run is performed?
If you’re generating the files with pdb2gmx as your first step, it should generate a position restraint file (posre.itp). You can edit this file to only include those atoms you want to constrain, and as long as the topology file includes it under a #include line and the mdp file calls it using the define = -DPOSRES line. The position restraint file specifies atoms based on the atom number, the topol.top file should tell you which atoms were assigned which numbers