Gromacs not maintaining the bond angles of arginine during energy minimization

[PanyueW]

GROMACS version: 2022.1
GROMACS modification: No
I am trying to run MD using a neutral system where all charged residues are neutralized. For example, I will have deprotonated arginines in my protein. I am not able to maintain bond angles of arginine residues when running energy minimization.
Here’s my mdp file:
; minim.mdp - used as input into grompp to generate em.tpr
; Parameters describing what to do, when to stop and what to save
define = -DPOSRES
integrator = steep ; Algorithm (steep = steepest descent minimization)
emtol = 1000.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm
emstep = 0.01 ; Minimization step size
nsteps = 5000 ; Maximum number of (minimization) steps to perform

; no COM motion removal because we have posres
comm-mode = None

; Parameters describing how to find the neighbors of each atom and how to calculate the interactions
nstlist = 1 ; Frequency to update the neighbor list and long range forces
cutoff-scheme = Verlet ; Buffered neighbor searching
ns_type = grid ; Method to determine neighbor list (simple, grid)
coulombtype = PME ; Treatment of long range electrostatic interactions
rcoulomb = 1.0 ; Short-range electrostatic cut-off
rvdw = 1.0 ; Short-range Van der Waals cut-off
pbc = xyz ; Periodic Boundary Conditions in all 3 dimensions
constraints = all-bonds
I would get LINCS errors for this setup.
Here’s a comparison of one arginine before/after energy minimization:

I am using charmm36-july-2021 for my simulation.
Is there a way to solve this problem?

[jalemkul]

The CHARMM residue definition for ARGN is buggy in the port for GROMACS. There is no solution yet, though I have identified the problem. I’m afraid it simply won’t be possible to simulate this species in GROMACS for the time being, sorry. CHARMM (the software) does some very weird patching to make ARGN work and translating that into something functional in GROMACS is not straightforward.