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
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