GROMACS modification: No
Hi everyone, I am currently working with a protein which has 6 Cu ions coordinated in its structure, I would like to know how I need to correctly run the simulation because it’s my first time running a MDS considering ions too. Among the solution I red there is the possibility to use harmonic restraint to restrain the Cu ions to the residues to which they are coordinated using [bonds] type 6 in the topology file. To apply this type of restraint I saw that for a correct syntax I need to specify the values of distance b0(nm) and the force [ kJ(mol)-1(nm)-2 ], I was wondering how to choose these 2 values. For the distance can I measure from the pdb the distance between the Cu and the atoms to which are coordinated and consider those values? While for the force how can I decide which value I need to use?