Bond restraint

GROMACS version:5.1.5
GROMACS modification: No
Here post your question: How to restrain bonds with simple harmonic potential?

Hi users,
I am working upon protein-protein simulation with GB1 and Lysozyme where I have taken 5 molecules of Lysozyme and 1 molecule of GB1 and I want to restrain all the bonds of all 5 lysozyme. For this, do I need to generate a distance restraint itp file through genrestr or any other procedure?
Can someone please guide me through the procedures to be done?



Bonds are already modeled by a harmonic potential, and restraints are not applied to bonds (constraints are, but those are different). Distance restraints are different still, but are not typically applied to bonds, because they would be redundant with the actual covalent bonds. Can you explain in greater detail what it is you’re trying to do?

I want to study the influence of increasing concentration of lysozyme on GB1 structure. In this I want the orientations of the bonds of lysozyme to be fixed so that there wouldn’t be any structural changes in the lysozyme during the simulation. Please suggest me how can I do it.

To put constraints on the bonds I can get it that it can be done through the *.mdp file but I want to put constraints only on lysozyme bonds and not on GB1 bonds. Can you please suggest me how can I put constraints on the selected bonds?

Constraining bonds does not preserve their relative orientation. The shortcut way to do this is simply to apply position restraints to lysozyme, but not GB1. Then the orientations of everything will remain relatively constant.

Ok. Thank you.