It has been described a bad modelling parameters for some ions in the AMBER FF. In simulations with high concentration of these ions, they tend to aggregate instead of remaining totally disolved (as expected at the concentrations worked).
This paper describes this fenomena and gives new parameters that improve the behaviour of these atoms: Cheatham's JPCB 2008
It might be sometimes interesting to know the equilibrium distance between two atom types.
In this post I will explain how to restraint the whole protein for running a MD using NAMD.
For applying harmonic restraints in NAMD we need to generate a PDB file of the system in which we indicate the atoms that we want to be restrained and the force to be applied.