GROMACS version: GROMACS2018
GROMACS modification: No
Dear GMX users,
I am trying to parameterise a Morse potential between two atoms of two different molecules. To do so, I performed QM calculations to obtain reasonable b0, D and beta parameters. Then, I built the GMX topology by adding the parameters of the two molecules togethers and added a morse bond description in the [bonds] section in the topology.
It looks like this:
[ bonds ]
; Morse potential
; ai aj funct r (b0 / nm) D (kJ/mol-1) beta(nm-1)
1 78 3 2.0000e-01 148.50 1.0000e+05;
I must be missing some steps here because the simulations do not crash and the bond breaks. However it always breaks no matter how big is the D value.
Should it add something else to the topology? I would be very grateful if you could offer some guidance.
Thank you in advance,