Penalty restricted dynamics in gromacs

User discussions
1

Hi all,

I am curious if gromacs can isssue penalty on some undesired motions. lets say if i have to restrict motion of protein to a confined space or steering a molecule in z direction without using force. I got to know that we can define penalties to undesired motions in dynamics. Can someone guide me through it?
are there any tricks for it? please suggest, thank you in advance.

2

Hi,
it depends on what you exactly want but you can have a look at the restraints ( see Restraints — GROMACS 2021.3 documentation) or to the option of the pull code (Non-equilibrium pulling — GROMACS 2021.3 documentation)
\Alessandra