[gmx-users] number of harmonic restraint

[Alexander Alexander]

Dear Gromacs user,

In free energy calculation of molecules(here amino acid) in waters
solution, people usually apply harmonic restrains between some of atoms in
the first step making it ready for removing charge and vdW in the next
steps. My question is that how many harmonic restrains are usually enough
to be interdicted between atoms to fulfill the conditions? If really
between each pair of atoms in amino acid is necessary?

Thanks,
Alex