[gmx-users] NPT error

[Albert]

Hi:

  I am following the tutorial:

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/07_equil2.html

the nvt step goes well, but the NPT always doesn't work. it said:


Program mdrun_mpi_bg, VERSION 4.5.5
Source code file: ../../../src/mdlib/domdec.c, line: 2633

Fatal error:
Step 2970: The domain decomposition grid has shifted too much in the 
Y-direction around cell 2 3 1

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

"Ich Bin Ein Berliner" (J.F. Kennedy)

Error on node 81, will try to stop all the nodes
Halting parallel program mdrun_mpi_bg on CPU 81 out of 128

gcq#193: "Ich Bin Ein Berliner" (J.F. Kennedy)

Abort(-1) on node 81 (rank 81 in comm 1140850688): application called 
MPI_Abort(MPI_COMM_WORLD, -1) - process 8
1
<Jan 06 05:47:13.496560> BE_MPI (ERROR): The error message in the job 
record is as follows:
<Jan 06 05:47:13.496622> BE_MPI (ERROR):   "killed with signal 6"

here is my NPT.mdp file:

title        = OPLS Lysozyme NPT equilibration
define        = -DPOSRES    ; position restrain the protein
; Run parameters
integrator    = md        ; leap-frog integrator
nsteps        = 100000    ; 2 * 100000 = 200 ps
dt        = 0.002        ; 1 fs
; Output control
nstxout        = 100        ; save coordinates every 0.2 ps
nstvout        = 100        ; save velocities every 0.2 ps
nstenergy    = 100        ; save energies every 0.2 ps
nstlog        = 100        ; update log file every 0.2 ps
; Bond parameters
continuation    = yes        ; Restarting after NVT
constraint_algorithm = lincs    ; holonomic constraints
constraints    = all-bonds    ; all bonds (even heavy atom-H bonds) 
constrained
lincs_iter    = 1        ; accuracy of LINCS
lincs_order    = 4        ; also related to accuracy
; Neighborsearching
ns_type        = grid        ; search neighboring grid cells
nstlist        = 5        ; 10 fs
rlist        = 1.0        ; short-range neighborlist cutoff (in nm)
rcoulomb    = 1.0        ; short-range electrostatic cutoff (in nm)
rvdw        = 1.0        ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype    = PME        ; Particle Mesh Ewald for long-range 
electrostatics
pme_order    = 4        ; cubic interpolation
fourierspacing    = 0.16        ; grid spacing for FFT
; Temperature coupling is on
tcoupl        = V-rescale    ; modified Berendsen thermostat
tc-grps        = Protein Non-Protein    ; two coupling groups - more 
accurate
tau_t        = 0.1    0.1    ; time constant, in ps
ref_t        = 300     300    ; reference temperature, one for each 
group, in K
; Pressure coupling is on
pcoupl        = Parrinello-Rahman    ; Pressure coupling on in NPT
pcoupltype    = isotropic    ; uniform scaling of box vectors
tau_p        = 2.0        ; time constant, in ps
ref_p        = 1.0        ; reference pressure, in bar
compressibility = 4.5e-5    ; isothermal compressibility of water, bar^-1
; Periodic boundary conditions
pbc        = xyz        ; 3-D PBC
; Dispersion correction
DispCorr    = EnerPres    ; account for cut-off vdW scheme
; Velocity generation
gen_vel        = no        ; Velocity generation is off
;warning
refcoord_scaling = all


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