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

[Justin A. Lemkul]

Which version of CVS are you using?  (This sounds like a question for the 
gmx-developers listserv.)  I believe this problem was fixed in CVS over a month ago:

http://www.gromacs.org/pipermail/gmx-developers/2008-July/002608.html

Although there is a possibility that something is really wrong, which Berk 
mentions in that post.

-Justin

Rebeca García Fandiño wrote:
> Hello,
> 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 nodes
> Halting 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):Busy
> srun: error: s23c2b13: task15: Exited with exit code 1
> MX:s23c2b06:Remote endpoint is closed, peer=00:60:dd:48:46:62 (s23c2b13:0)
> srun: error: s23c2b06: task11: Exited with exit code 1
> srun: error: s23c2b13: task[12-14]: Killed
> srun: 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           = EQUILIBRADO
> cpp             = /usr/bin/cpp
> include         = -I../top
> define          = -DPOSRES_D -DPOSRES_P
> constraints     = all-bonds
> integrator      = md
> dt              = 0.002
> nsteps          = 10000
> nstxout         = 1000
> nstvout         = 1000
> nstlog          = 1000
> nstenergy       = 1000
> nstxtcout       = 1000
> nstlist         = 10
> ns_type         = grid
> rlist           = 1.0
> coulombtype     = PME
> rcoulomb        = 1.0
> vdwtype         = cut-off
> rvdw            = 1.4
> pme_order       = 4
> ewald_rtol      = 1e-5
> optimize_fft    = yes
> ;Berendsen temperature coupling is on
> Tcoupl          = berendsen
> tau_t           = 0.1     0.1    0.1
> tc-grps         = Protein dop SOL_Na_Cl
> ref_t           = 310     310    310
> ; Pressure coupling
> Pcoupl                   = Parrinello-Rahman
> Pcoupltype               = Semiisotropic
> ; Time constant (ps), compressibility (1/bar) and reference P (bar)
> tau-p                    = 1.0 1.0
> compressibility          = 4.6E-5 4.6E-5
> ref-p                    = 1.0 1.0
> ;Generate velocities is on at 310 K
> gen_vel         = yes
> gen_temp        = 310
> gen_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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-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================