Is it possible to run a local MD in a big system?

User discussions
1

GROMACS version: 2020
GROMACS modification: Yes/No

Hi guys, I need to run a MD simulation of a ribosomal subunit in complex with a ligand. Since I am only interested in the mechanism and stability of the ligand in the complex, I was wondering if it is possible to run a sort of local MD of the ligand and the region around it, with explicit solvent; leaving the rest of the subunit “frozen”? I would like to do this, because I do not have all the computational power needed for the MD simulation of whole system. Any suggestion is welcome.
Thanks in advance
Cheers

2

You can freeze part of the atoms, but unfortunately this will not make your simulation run faster with GROMACS.

3

Thanks @hess for your prompt response. Any other method I could use?

4

Some studies on the ribosome extract the part of interest from an experimental structure with some margin, and add position restraint on the margins (force constant linked to RMSF) while the center is free. See this for instance (subheading Molecular Dynamics Simulations).