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<body class='hmmessage'><div style="text-align: left;">Hi,<br><br>This sounds like the bug in domdec.c that I fixed a month ago:<br>revision 1.146<br></div>date: 2008/07/11 12:09:43; author: hess; state: Exp; lines: +307 -193<br>fixed incorrect computation of the PME coordinate communication range with dlb and change some formatting<br><br>Is your version from before that date?<br><br>Berk.<br><br><br><hr id="EC_stopSpelling">From: regafan@hotmail.com<br>To: gmx-users@gromacs.org<br>Date: Tue, 12 Aug 2008 17:15:59 +0000<br>Subject: [gmx-users] error: 1 particles communicated to PME node 3 (...)<br><br>
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Hello,<br>
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:<br>
<br>
<br>
Fatal error:<br>1 particles communicated to PME node 3 are more than a cell length out of the domain decomposition cell of their charge group<br>-------------------------------------------------------<br>
"O My God, They Killed Kenny !" (South Park)<br>
Error on node 15, will try to stop all the nodes<br>Halting parallel program mdrun_mpi on CPU 15 out of 32<br>
gcq#254: "O My God, They Killed Kenny !" (South Park)<br>
[15] MPI Abort by user Aborting program !<br>mx_finalize() called while some endpoints are still open.<br>MX:s23c2b13:mx_finalize:error 20(errno=2):Busy<br>srun: error: s23c2b13: task15: Exited with exit code 1<br>MX:s23c2b06:Remote endpoint is closed, peer=00:60:dd:48:46:62 (s23c2b13:0)<br>srun: error: s23c2b06: task11: Exited with exit code 1<br>srun: error: s23c2b13: task[12-14]: Killed<br>srun: Job Failed<br>
<br>
The calculations stops after 2000 steps:<br>
<br>
Step Time Lambda<br> 2000 4.00000 0.00000<br>
Energies (kJ/mol)<br> Angle Ryckaert-Bell. LJ-14 Coulomb-14 LJ (SR)<br> 6.17238e+05 4.06472e+05 1.89810e+05 5.82538e+05 3.71263e+06<br> LJ (LR) Coulomb (SR) Coul. recip. Position Rest. Potential<br> -5.12910e+04 -9.09326e+06 -1.97121e+06 1.69698e+06 -3.91010e+06<br> Kinetic En. Total Energy Temperature Pressure (bar) Cons. rmsd ()<br> 2.12885e+06 -1.78125e+06 3.56627e+02 -2.35301e+04 2.99204e-05<br>
<br>
As input I use:<br>
<br>
title = EQUILIBRADO<br>cpp = /usr/bin/cpp<br>include = -I../top<br>define = -DPOSRES_D -DPOSRES_P<br>constraints = all-bonds<br>integrator = md<br>dt = 0.002<br>nsteps = 10000<br>nstxout = 1000<br>nstvout = 1000<br>nstlog = 1000<br>nstenergy = 1000<br>nstxtcout = 1000<br>nstlist = 10<br>ns_type = grid<br>rlist = 1.0<br>coulombtype = PME<br>rcoulomb = 1.0<br>vdwtype = cut-off<br>rvdw = 1.4<br>pme_order = 4<br>ewald_rtol = 1e-5<br>optimize_fft = yes<br>;Berendsen temperature coupling is on<br>Tcoupl = berendsen<br>tau_t = 0.1 0.1 0.1<br>tc-grps = Protein dop SOL_Na_Cl<br>ref_t = 310 310 310<br>; Pressure coupling<br>Pcoupl = Parrinello-Rahman<br>Pcoupltype = Semiisotropic<br>; Time constant (ps), compressibility (1/bar) and reference P (bar)<br>tau-p = 1.0 1.0<br>compressibility = 4.6E-5 4.6E-5<br>ref-p = 1.0 1.0<br>;Generate velocities is on at 310 K<br>gen_vel = yes<br>gen_temp = 310<br>gen_seed = 173529<br><br>
Does anybody which could be the problem?<br>
<br>
Thank you very much for your help.<br>
<br>
Best wishes,<br>
<br>
Rebeca Garcia Fandiño<br>
Parc Cientific de Barcelona<br><br>
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