Using external harmonic potential

GROMACS version: 2016-4

Hello everyone,

I have a simulation box containing a layer of molecules in water. I want to use an external harmonic potential to the molecules to keep them still as a layer in water during NPT equilibration and MD production runs. Is it possible to do this using GROMACS mdp parameters or do I need to use coding?

Thank you in advance for any helps.

Please let me know if I should provide extra information about my simulation box.


I guess you would like to use position restraints.
When generated, you need to then let grompp know you are using restraints, by modifying the .mdp file. You might find this tutorial useful for an example.

Hi Ali,
Thank you for your help. I will try it.