Constraints Option with Flat-Bottom Position Restraints in mdp file

User discussions
1

GROMACS version:
Hello,

I have a question regarding the constraints option in the .mdp file.
When using flat-bottom position restraints in MD simulations with the AMBER force field, is it necessary to set constraints = all-bonds, or can I use constraints = h-bonds instead?

Thank you in advance for your assistance!

Best regards,

2

Use the constraint convention that the force field was parametrized to use. For AMBER, that is constraints = h-bonds. If you constrain bonds inappropriately, you can imbalance the subtle vibrational forces of the model.

3

thank you so much