GROMACS version: 2024.1
GROMACS modification: No
Hello everyone,
I have a molecule CH3 - NH3, whose atomic positions are known. I want to perform a simulation with this molecule being completely rigid (i.e., relative position of all atoms in the molecule is fixed).
Naturally, I tried to use constraints for this. I speciify bond and angle terms, and use the constraints = h-angles option in mdp file to convert the bonds and angle in the molecules to constraints.
But, when I run the dynamics, it gives me lincs error as follows:
‘relative constraint deviation after LINCS’
If I change the .itp file for the molecule to only include the bond constraints, instead of using h-angles option in the mdp file, the simulation runs fine. But the molecule does not remain rigid.
PS: I do not have the exact bond and angle constants to first use with energy minimization, and hence have to directly run an NVT simulation or run minimization with constraints.