Impose LINCS algorithm for specific type of molecule instead of whole simulation box

User discussions
1

GROMACS version: 2019
GROMACS modification: Yes/No
Hi

I am using gromacs software. In order to minimize my simulation box, I need to impose the LINCS algorithm for a specific type of molecule. Existence of water molecules in the simulation box results in LINCS warning, about 50 warnings, But the minimization does not stop.

Is there any option to implement all-bond constraints on a specific type of molecule instead of the entire simulation box (all molecules)?

Can I go on without paying attention to warnings?

For constrained bonds, I only have Equilibrated bond length, since lack of force constant, I have to use independent value for force constant because it caused the error.

thanks in advance

Nasrolla

2

You can globally disable constraints with constraints = none and then add [constraints] to any molecule topology to specifically invoke only those constraints.