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?