Parameterising a Morse potential

User discussions
1

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,

Salome

2

Hi,

To put a bond between two molecules these molecules should defined as one molecule. Is it what you did when you wrote

In general it is good to check definition of the parameter of the morse potential as defined in gromacs (https://manual.gromacs.org/current/reference-manual/functions/bonded-interactions.html?highlight=morse%20potential) and the units

Best regards
Alessandra

3

Dear Alessandra,

Thank you for your answer.

You were right I had messed up the parameters of the Morse potential. I have fixed that and it works.

Thanks again,
Best regards,

Salomé

4

Dear Salomé,
I want to use Morse potential to simulate the bond breaking. I have the same problem with you. I want to know how you solve this problem.
Thank you in advance!
Best regards,
Asuka