Equilibration issue with GROMACS 2024.1

User discussions
1

I’m encountering an error while equilibrating my system using GROMACS 2024.1:

“Error: One or more atoms moved too far between two domain decomposition steps.”

System Details:

  • Protein: Octameric protein (only functional in this state)
  • Structures: Cryo-EM and X-ray crystal structures resolved (wild-type)
  • Goal: Study effect of mutations using Molecular Dynamics (MD)

To resolve this issue, I’ve tried:

  1. Changing box type from dodecahedron to cubic with buffer distances (1.0, 1.2, and 1.4) to the edge, ensuring centered positioning.
  2. Alternative barostat algorithms: Berendsen (200ps) before switching to Parrinello-Rahman.

However, these adjustments haven’t resolved the issue. Notably, GROMACS 2023.3 works perfectly for this system.

Previous discussions on similar topics haven’t provided a working solution for my system.

Could you please assist me in resolving this equilibration issue with GROMACS 2024.1?

Thank you for your time and expertise.

define = -DPOSRES ; position restrain the protein and ligand
; Run parameters
integrator = md ; leap-frog integrator
nsteps = 100000 ; 2 * 100000 = 200 ps
dt = 0.002 ; 2 fs
; Output control
nstxout = 2500 ; save coordinates every 5.0 ps
nstvout = 500 ; save velocities every 1.0 ps
nstenergy = 500 ; save energies every 1.0 ps
nstlog = 500 ; update log file every 1.0 ps
; Bond parameters
continuation = yes ; continuing after NVT
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
; Nonbonded settings
cutoff-scheme = Verlet ; Buffered neighbor searching
ns_type = grid ; search neighboring grid cells
nstlist = 10 ; 20 fs, largely irrelevant with Verlet scheme
rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm)
rvdw = 1.2 ; short-range van der Waals cutoff (in nm)
DispCorr = EnerPres ; account for cut-off vdw scheme
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
pme_order = 4 ; cubic interpolation
fourierspacing = 0.16 ; grid spacing for FFT
; Temperature coupling is on
tcoupl = V-rescale ; modified Berendsen thermostat
tc-grps = Protein Non-protein ; two coupling groups - more accurate
tau_t = 0.1 0.1 ; time constant, in ps
ref_t = 300 300 ; reference temperature, one for each group, in K
; Pressure coupling is on
pcoupl = Parrinello-Rahman ; pressure coupling on in NPT
pcoupltype = isotropic ; uniform scaling of box vectors
tau_p = 2.0 ; time constant, in ps
ref_p = 1.0 ; reference pressure, in bar
compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1
refcoord_scaling = com
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
; Velocity generation
gen_vel = no ; velocity generation is off

2

I assume that the system is exploding and I think the pressure coupling is the problem. Unless you’ve done multiple repeats of the simulation in both 2023.3 and 2024.1 and see a clear trend that it’s working in the former, but not the latter, I think its just chance that explains the difference.

There are a few things I would recommend trying:

  • Switch to the c-rescale barostat
    Or
  • Longer equilibration (2-10 ns) with Berendsen, if you must use Parrinello-Rahman
  • If you must use Parrinello-Rahman set tau-p = 10
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