About Morse potential

User discussions
1

GROMACS version: 2018.7
GROMACS modification: No

Dear GMX users,

I would like to run MD simulations of a system under the external electric field. I want to use Morse potential for the specific bond in the molecules. I am very new for these kind of calculations. If possible, please advice me to set correct input mdp file.
I have following two questions:

  1. How can I include the Morse in a mdp file?

  2. Is it possible to use the Morse potential for only a type of bonds in the molecules?

Best regards,

Mijiddorj

2

Hi,

How can I include the Morse in a mdp file?

No, bond and non bonded parameters are defined in the topology and force field files.

Is it possible to use the Morse potential for only a type of bonds in the molecules?

Yes, the Morse function for bond is implemented in GROMACS.
You can define the bond parameters and functions directly in the topololgy file under directive [ bonds ] for each bond you want a specific Morse potential ( for example if the bonds in discussion are few), otherwise you can modify the bond type in the force field.

Please have a look at
http://manual.gromacs.org/current/reference-manual/topologies/topology-file-formats.html?highlight=force%20field%20table
In Table 14 you find for the syntax for bond

A general warning, one has to pay a lot of attention before modifying force field parameter/function. New parameters have to be developed in line with the original force field philosophy.

Best regards
Alessandra

3

Dear Alevilla,

Thank you very much for your kind reply.

Best regards,

Mijiddorj