[gmx-users] error: 1 particles communicated to PME node 3 (...)

Rebeca García Fandiño regafan at hotmail.com
Tue Aug 12 19:15:59 CEST 2008

I am trying to equilibrate a protein+membrane system in Gromacs 4. The minimization went OK, but in the equilibration at constant pressure I got this error:
Fatal error:1 particles communicated to PME node 3 are more than a cell length out of the domain decomposition cell of their charge group-------------------------------------------------------
"O My God, They Killed Kenny !" (South Park)
Error on node 15, will try to stop all the nodesHalting parallel program mdrun_mpi on CPU 15 out of 32
gcq#254: "O My God, They Killed Kenny !" (South Park)
[15] MPI Abort by user Aborting program !mx_finalize() called while some endpoints are still open.MX:s23c2b13:mx_finalize:error 20(errno=2):Busysrun: error: s23c2b13: task15: Exited with exit code 1MX:s23c2b06:Remote endpoint is closed, peer=00:60:dd:48:46:62 (s23c2b13:0)srun: error: s23c2b06: task11: Exited with exit code 1srun: error: s23c2b13: task[12-14]: Killedsrun: Job Failed
The calculations stops after 2000 steps:
           Step           Time         Lambda           2000        4.00000        0.00000
   Energies (kJ/mol)          Angle Ryckaert-Bell.          LJ-14     Coulomb-14        LJ (SR)    6.17238e+05    4.06472e+05    1.89810e+05    5.82538e+05    3.71263e+06        LJ (LR)   Coulomb (SR)   Coul. recip. Position Rest.      Potential   -5.12910e+04   -9.09326e+06   -1.97121e+06    1.69698e+06   -3.91010e+06    Kinetic En.   Total Energy    Temperature Pressure (bar)  Cons. rmsd ()    2.12885e+06   -1.78125e+06    3.56627e+02   -2.35301e+04    2.99204e-05
As input I use:
title           = EQUILIBRADOcpp             = /usr/bin/cppinclude         = -I../topdefine          = -DPOSRES_D -DPOSRES_Pconstraints     = all-bondsintegrator      = mddt              = 0.002nsteps          = 10000nstxout         = 1000nstvout         = 1000nstlog          = 1000nstenergy       = 1000nstxtcout       = 1000nstlist         = 10ns_type         = gridrlist           = 1.0coulombtype     = PMErcoulomb        = 1.0vdwtype         = cut-offrvdw            = 1.4pme_order       = 4ewald_rtol      = 1e-5optimize_fft    = yes;Berendsen temperature coupling is onTcoupl          = berendsentau_t           = 0.1     0.1    0.1tc-grps         = Protein dop SOL_Na_Clref_t           = 310     310    310; Pressure couplingPcoupl                   = Parrinello-RahmanPcoupltype               = Semiisotropic; Time constant (ps), compressibility (1/bar) and reference P (bar)tau-p                    = 1.0 1.0compressibility          = 4.6E-5 4.6E-5ref-p                    = 1.0 1.0;Generate velocities is on at 310 Kgen_vel         = yesgen_temp        = 310gen_seed        = 173529
Does anybody which could be the problem?
Thank you very much for your help.
Best wishes,
Rebeca Garcia Fandiño
Parc Cientific de Barcelona
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