# Fatal Domain Decomposition Cell Error during NVT Equilibration **URL:** \ **Category:** User discussions\ **Created:** [February 18, 2021, 10:48pm UTC](https://gromacs.bioexcel.eu/t/fatal-domain-decomposition-cell-error-during-nvt-equilibration/1617 "2021-02-18T22:48:31Z")\ **Posts on this page:** 4\ **Page:** 1
**Author:** ![jabode](https://avatars.discourse-cdn.com/v4/letter/j/e0b2c6/32.png) [@jabode](https://gromacs.bioexcel.eu/u/jabode)\ **Post date:** [February 18, 2021, 10:48pm UTC](https://gromacs.bioexcel.eu/t/fatal-domain-decomposition-cell-error-during-nvt-equilibration/1617/1 "2021-02-18T22:48:32Z")
GROMACS version: 2019.5 GROMACS modification: To my knowledge No Hello everyone, I am trying to prepare a system of 125 PEC6 (pentaerythritol tetrahexanoate) molecules for viscosity and free energy calculations. But every time I am running a NVT simulation over 10 ns, which I believe to be necessary to calculate the viscosity via EMD-methods, I get the following error message with varying PME ranks: Fatal error: "1 particles communicated to PME rank X are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension y. This usually means that your system is not well equilibrated." The initial configuration was produced by packmol, followed by an energy minimization. Thereafter I alternated between NpT and NVT to adjust the box size with 10 simulations รก 1 ns. After this I try to run the 10 ns equilibration, but everytime the fatal error occurs. I tried diffrent variations (e.g. with higher temperatures, lower density, diffrent values for tau\_t) but the fatal error persists. Now I am hoping to find some insight through the help of someone more experienced than me. Are there common mistakes which are leading to this kind of error? Thank you in advance! Jan edit: Strangely, NpT Simulations seem to run through the 10 ns without error. Following are the mdp options I am using: ;############################## Run control ############################## integrator = sd dt = 0.0005 nsteps = 20000000 ;############################## Minimization ############################# emtol = 10 emstep = 0.01 niter = 20 ;############################# Output Control ############################ nstcalcenergy = 100 nstenergy = 1000 nstlog = 10000 nstxout = 0 nstvout = 0 nstfout = 0 ;########################### Neighborsearching ########################### cutoff-scheme = verlet nstlist = 10 ns\_type = grid pbc = xyz rlist = 1.2 verlet-buffer-tolerance = 0.005 ;############################# Electrostatics ############################# coulombtype = PME coulomb-modifier = none rcoulomb = 1.2 pme\_order = 4 ewald\_rtol = 1e-05 epsilon\_surface = 0 fourierspacing = 0.12 ;############################## van der Waals ############################## vdwtype = cutoff vdw-modifier = none rvdw = 1.2 DispCorr = EnerPres ;########################### Temperature coupling ########################### ;tcoupl = is implicitly handled by the sd integrator tc\_grps = system tau\_t = 2.5 ref\_t = 373.15 ;############################ Velocity generation ############################ gen\_vel = yes gen\_temp = 373.15 gen\_seed = -1 ;################################### Bonds ################################### constraints = none continuation = no constraint-algorithm = lincs lincs-order = 4 ---
**Author:** ![alevilla](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/alevilla/32/439_2.png) [@alevilla](https://gromacs.bioexcel.eu/u/alevilla)\ **Post date:** [February 19, 2021, 7:41pm UTC](https://gromacs.bioexcel.eu/t/fatal-domain-decomposition-cell-error-during-nvt-equilibration/1617/2 "2021-02-19T19:41:04Z")
Hi, a question during equilibration, did you check that pressure and temperature are equilibrated during the 10 1ns-simulation? Best regards Alessandra ---
**Author:** ![jabode](https://avatars.discourse-cdn.com/v4/letter/j/e0b2c6/32.png) [@jabode](https://gromacs.bioexcel.eu/u/jabode)\ **Post date:** [February 21, 2021, 10:03pm UTC](https://gromacs.bioexcel.eu/t/fatal-domain-decomposition-cell-error-during-nvt-equilibration/1617/3 "2021-02-21T22:03:33Z")
Hello Alessandra, the system seemed somewhat equilibrated but there are some high spikes in temperature and a drift right at the end. So I started another 10 ns alternating simulation from the last step, but the error occured after 2 ns. Again during the NVT run. The pressure seems to be fine, but the temperature shows some very distinct spikes every now and then, also during the NpT runs. I analyzed the energies in the edr during one of those spikes and it seems to be mostly related to a high bond energy. Is my understanding correct, that this error usually occurs with instable systems and not so much because I chose the wrong decomposition cell distribution? Or a too high degree of parallelization? My guess right now would be that there is a mistake somewhere in the parametrization of the molecules, even though I double and triple checked, or the thermostat is overregulating the system. I also tried a Nose-Hoover thermostat but the error occurs there as well. Thank you very much for your reply Jan ---
**Author:** ![alevilla](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/alevilla/32/439_2.png) [@alevilla](https://gromacs.bioexcel.eu/u/alevilla)\ **Post date:** [February 22, 2021, 10:48am UTC](https://gromacs.bioexcel.eu/t/fatal-domain-decomposition-cell-error-during-nvt-equilibration/1617/4 "2021-02-22T10:48:28Z")
Hi, > Is my understanding correct, that this error usually occurs with instable systems and not so much because I chose the wrong decomposition cell distribution? Or a too high degree of parallelization? Diffucult to generalize, but I think that in your case the source of error is due to the system not yet well equilibrated. The reasons why a system has difficulty to equilibrate may be different. You wrote that you observed something strange in the bond energies. I can suggest (for example) to check that 1. the time step you use is compatible with the force field. Force field can be parameterized using contraints for h-bond (or all bonds). Then you have to active the option in the mdp file 2. if you have implement the force field, you can check that the bond parameter are corrected implemented (with correct units) Best regards Alessandra