How to decide on constant or restraint

User discussions
1

Hi everyone,

my goal is to constrain/restrain 2 atoms of a molecule during an mdrun. But I don’t know which kind of constraint /restraint I should use. I also have different confirmations of the molecule, where a certain bond (between those mentioned molecules) has always a different length. Can someone explain to me, which method I should use? (btw, I am new to this)

2

you need to apply restrain, you need to make the bond vibration within a certain limit without changing the natural dyanmics of the protein. Refer constrain and restrain section in gromacs manual.