# Equilibration issue with GROMACS 2024.1 **URL:** \ **Category:** User discussions\ **Created:** [November 20, 2024, 10:10pm UTC](https://gromacs.bioexcel.eu/t/equilibration-issue-with-gromacs-2024-1/10597 "2024-11-20T22:10:49Z")\ **Posts on this page:** 2\ **Page:** 1
**Author:** ![James007](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/james007/32/4180_2.png) [@James007](https://gromacs.bioexcel.eu/u/James007)\ **Post date:** [November 20, 2024, 10:10pm UTC](https://gromacs.bioexcel.eu/t/equilibration-issue-with-gromacs-2024-1/10597/1 "2024-11-20T22:10:49Z")
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 ---
**Author:** ![MagnusL](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/magnusl/32/2380_2.png) [@MagnusL](https://gromacs.bioexcel.eu/u/MagnusL)\ **Post date:** [November 21, 2024, 6:23am UTC](https://gromacs.bioexcel.eu/t/equilibration-issue-with-gromacs-2024-1/10597/2 "2024-11-21T06:23:42Z")
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`