How do I constrain or restrain a part of a molecule

User discussions
1

GROMACS version: 2021
GROMACS modification: Yes/No

I have a protein and I know the structure for a large part of it. I want to run an MD simulation on the rest of the protein. I know I can use LINCS to constrain a part of the molecule. However, in the standard md.mdp file, these are the bond parameters given:

; Bond parameters
continuation = yes ; Restarting after NPT
constraint_algorithm = lincs ; holonomic constraints
constraints = h-bonds ; bonds involving H are constrained
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy

To me, this suggests that LINCS is already active, but I’m not sure how.

How would I actually use LINCS to constrain a particular part of the molecule?

2

LINCS constrains bond lengths to apply a longer time step when integrating the equations of motion. What you probably want is to restrain the known part, and you can use [ position_restraints ] for that, simply deleting atoms (or whole sections within chosen [ moleculetype ]s) that you want to keep mobile.