Units

For polarizable models α=K_c q²/k,  where K_c is the coulomb constant and k is the elastic constant of the spring. The coulomb constant is:

• K_c=14.399629·10^-3 if the elastic constant is in eV/A² and charges are in fundamental charge units.

FORCE FIELDS

It is perfectly and nicely explained in the manual... but you must search it in two different chapters. I gather the info about forcefields... I keep forgeting this basics always:

 

Lennard Jones:

Normally I use combination rule 2 in Gromacs(σ_AB=(σ_A+σ_B)/2 ; ε_AB=(ε_A·ε_B)^1/2  In this case:

U_LJ=4ε[(σ/r)¹²-(σ/r)⁶]=ε[(r₀/r)¹² -(r₀/r)⁶ ]

And the units [σ]=nm and [ε]=kj/mol being σ the distance for which the potential is zero.

An alternative way of writing the potetial is using the distance related to the minimum of the potential r₀. The relation between r and σ is easy: 

r₀=2^1/6σ

Please, look in this page above if you need to transform units. Click here if you want to know the relationship with amber.

Buckingham:

Buckingham is defined as A exp(-r/ρ)-C/r6 in most paper. WARNING in gromacs is defined as Aexp(-Br)-C/r6. That means that you must inverse ρ and (usually) change units!!!!

There is a way to obtain the parameters from buckingham to LJ and vice versa. This should not be used unless a case of extreme necessity: of course you will loose information and this should only be done in the case the repulsive side of your potential is not important (i.e. pressure can be affected!)