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<font size="+1"><font face="WenQuanYi WenQuanYi Bitmap Song">Hi:<br>
<br>
I am following the tutorial:<br>
<br>
<a class="moz-txt-link-freetext" href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/07_equil2.html">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/07_equil2.html</a><br>
<br>
the nvt step goes well, but the NPT always doesn't work. it
said:<br>
<br>
<br>
Program mdrun_mpi_bg, VERSION 4.5.5<br>
Source code file: ../../../src/mdlib/domdec.c, line: 2633<br>
<br>
Fatal error:<br>
Step 2970: The domain decomposition grid has shifted too much in
the Y-direction around cell 2 3 1<br>
<br>
For more information and tips for troubleshooting, please check
the GROMACS<br>
website at <a class="moz-txt-link-freetext" href="http://www.gromacs.org/Documentation/Errors">http://www.gromacs.org/Documentation/Errors</a><br>
-------------------------------------------------------<br>
<br>
"Ich Bin Ein Berliner" (J.F. Kennedy)<br>
<br>
Error on node 81, will try to stop all the nodes<br>
Halting parallel program mdrun_mpi_bg on CPU 81 out of 128<br>
<br>
gcq#193: "Ich Bin Ein Berliner" (J.F. Kennedy)<br>
<br>
Abort(-1) on node 81 (rank 81 in comm 1140850688): application
called MPI_Abort(MPI_COMM_WORLD, -1) - process 8<br>
1<br>
<Jan 06 05:47:13.496560> BE_MPI (ERROR): The error message
in the job record is as follows:<br>
<Jan 06 05:47:13.496622> BE_MPI (ERROR): "killed with
signal 6"<br>
<br>
here is my NPT.mdp file:<br>
<br>
title = OPLS Lysozyme NPT equilibration <br>
define = -DPOSRES ; position restrain the protein<br>
; Run parameters<br>
integrator = md ; leap-frog integrator<br>
nsteps = 100000 ; 2 * 100000 = 200 ps<br>
dt = 0.002 ; 1 fs<br>
; Output control<br>
nstxout = 100 ; save coordinates every 0.2 ps<br>
nstvout = 100 ; save velocities every 0.2 ps<br>
nstenergy = 100 ; save energies every 0.2 ps<br>
nstlog = 100 ; update log file every 0.2 ps<br>
; Bond parameters<br>
continuation = yes ; Restarting after NVT <br>
constraint_algorithm = lincs ; holonomic constraints <br>
constraints = all-bonds ; all bonds (even heavy atom-H
bonds) constrained<br>
lincs_iter = 1 ; accuracy of LINCS<br>
lincs_order = 4 ; also related to accuracy<br>
; Neighborsearching<br>
ns_type = grid ; search neighboring grid cells<br>
nstlist = 5 ; 10 fs<br>
rlist = 1.0 ; short-range neighborlist cutoff (in
nm)<br>
rcoulomb = 1.0 ; short-range electrostatic cutoff (in
nm)<br>
rvdw = 1.0 ; short-range van der Waals cutoff (in
nm)<br>
; Electrostatics<br>
coulombtype = PME ; Particle Mesh Ewald for long-range
electrostatics<br>
pme_order = 4 ; cubic interpolation<br>
fourierspacing = 0.16 ; grid spacing for FFT<br>
; Temperature coupling is on<br>
tcoupl = V-rescale ; modified Berendsen thermostat<br>
tc-grps = Protein Non-Protein ; two coupling groups -
more accurate<br>
tau_t = 0.1 0.1 ; time constant, in ps<br>
ref_t = 300 300 ; reference temperature, one for
each group, in K<br>
; Pressure coupling is on<br>
pcoupl = Parrinello-Rahman ; Pressure coupling on in
NPT<br>
pcoupltype = isotropic ; uniform scaling of box vectors<br>
tau_p = 2.0 ; time constant, in ps<br>
ref_p = 1.0 ; reference pressure, in bar<br>
compressibility = 4.5e-5 ; isothermal compressibility of
water, bar^-1<br>
; Periodic boundary conditions<br>
pbc = xyz ; 3-D PBC<br>
; Dispersion correction<br>
DispCorr = EnerPres ; account for cut-off vdW scheme<br>
; Velocity generation<br>
gen_vel = no ; Velocity generation is off <br>
;warning<br>
refcoord_scaling = all<br>
<br>
<br>
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