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 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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