On 5/16/15 6:27 AM, James Lord wrote:
Dear gmx users,
I am getting this error, Can anyone help me to get around this?
Cheers
James
Program mdrun, VERSION 4.6.3
Source code file: /home/james/gromacs-4.6.3/src/mdlib/domdec.c, line: 6792
Fatal error:
There is no domain decomposition for 8 nodes that is compatible with the
given box and a minimum cell size of 6.93203 nm
Change the number of nodes or mdrun option -rdd
Look in the log file for details on the domain decomposition
Log file opened on Sat May 16 22:15:44 2015
Host: james-E530 pid: 22300 nodeid: 0 nnodes: 1
Gromacs version: VERSION 4.6.3
Precision: single
Memory model: 64 bit
MPI library: thread_mpi
OpenMP support: enabled
GPU support: disabled
invsqrt routine: gmx_software_invsqrt(x)
CPU acceleration: AVX_256
FFT library: fftw-3.3.2-sse2
Large file support: enabled
RDTSCP usage: enabled
Built on: Wed Oct 30 18:28:46 NZDT 2013
Built by: james@james-E530 [CMAKE]
Build OS/arch: Linux 3.11.0-12-generic x86_64
Build CPU vendor: GenuineIntel
Build CPU brand: Intel(R) Core(TM) i7-3632QM CPU @ 2.20GHz
Build CPU family: 6 Model: 58 Stepping: 9
Build CPU features: apic avx clfsh cmov cx8 cx16 f16c htt lahf_lm mmx msr
nonstop_tsc pcid pclmuldq pdcm popcnt pse rdrnd rdtscp sse2 sse3 sse4.1
sse4.2 ssse3 tdt x2apic
C compiler: /usr/bin/cc GNU cc (Ubuntu/Linaro 4.8.1-10ubuntu8) 4.8.1
C compiler flags: -mavx -Wextra -Wno-missing-field-initializers
-Wno-sign-compare -Wall -Wno-unused -Wunused-value -Wno-unused-parameter
-Wno-array-bounds -Wno-maybe-uninitialized -Wno-strict-overflow
-fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast -O3
-DNDEBUG
:-) G R O M A C S (-:
Gromacs Runs On Most of All Computer Systems
:-) VERSION 4.6.3 (-:
Contributions from Mark Abraham, Emile Apol, Rossen Apostolov,
Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar,
Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph Junghans,
Peter Kasson, Carsten Kutzner, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,
Berk Hess, David van der Spoel, and Erik Lindahl.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2012,2013, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.
:-) mdrun (-:
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl
GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable
molecular simulation
J. Chem. Theory Comput. 4 (2008) pp. 435-447
-------- -------- --- Thank You --- -------- --------
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C.
Berendsen
GROMACS: Fast, Flexible and Free
J. Comp. Chem. 26 (2005) pp. 1701-1719
-------- -------- --- Thank You --- -------- --------
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
E. Lindahl and B. Hess and D. van der Spoel
GROMACS 3.0: A package for molecular simulation and trajectory analysis
J. Mol. Mod. 7 (2001) pp. 306-317
-------- -------- --- Thank You --- -------- --------
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
H. J. C. Berendsen, D. van der Spoel and R. van Drunen
GROMACS: A message-passing parallel molecular dynamics implementation
Comp. Phys. Comm. 91 (1995) pp. 43-56
-------- -------- --- Thank You --- -------- --------
Input Parameters:
integrator = steep
nsteps = 50000
init-step = 0
cutoff-scheme = Group
ns_type = Grid
nstlist = 5
ndelta = 2
nstcomm = 100
comm-mode = Linear
nstlog = 1000
nstxout = 0
nstvout = 0
nstfout = 0
nstcalcenergy = 100
nstenergy = 1000
nstxtcout = 0
init-t = 0
delta-t = 0.001
xtcprec = 1000
fourierspacing = 0.12
nkx = 56
nky = 56
nkz = 144
pme-order = 4
ewald-rtol = 1e-05
ewald-geometry = 0
epsilon-surface = 0
optimize-fft = FALSE
ePBC = xyz
bPeriodicMols = FALSE
bContinuation = FALSE
bShakeSOR = FALSE
etc = No
bPrintNHChains = FALSE
nsttcouple = -1
epc = No
epctype = Isotropic
nstpcouple = -1
tau-p = 1
ref-p (3x3):
ref-p[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
ref-p[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
ref-p[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
compress (3x3):
compress[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
compress[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
compress[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
refcoord-scaling = No
posres-com (3):
posres-com[0]= 0.00000e+00
posres-com[1]= 0.00000e+00
posres-com[2]= 0.00000e+00
posres-comB (3):
posres-comB[0]= 0.00000e+00
posres-comB[1]= 0.00000e+00
posres-comB[2]= 0.00000e+00
verlet-buffer-drift = 0.005
rlist = 0.9
rlistlong = 1.4
nstcalclr = 5
rtpi = 0.05
coulombtype = PME
coulomb-modifier = None
rcoulomb-switch = 0
rcoulomb = 0.9
vdwtype = Cut-off
vdw-modifier = None
rvdw-switch = 0
rvdw = 1.4
epsilon-r = 1
epsilon-rf = inf
tabext = 1
implicit-solvent = No
gb-algorithm = Still
gb-epsilon-solvent = 80
nstgbradii = 1
rgbradii = 1
gb-saltconc = 0
gb-obc-alpha = 1
gb-obc-beta = 0.8
gb-obc-gamma = 4.85
gb-dielectric-offset = 0.009
sa-algorithm = Ace-approximation
sa-surface-tension = 2.05016
DispCorr = No
bSimTemp = FALSE
free-energy = no
nwall = 0
wall-type = 9-3
wall-atomtype[0] = -1
wall-atomtype[1] = -1
wall-density[0] = 0
wall-density[1] = 0
wall-ewald-zfac = 3
pull = no
rotation = FALSE
disre = No
disre-weighting = Conservative
disre-mixed = FALSE
dr-fc = 1000
dr-tau = 0
nstdisreout = 100
orires-fc = 0
orires-tau = 0
nstorireout = 100
dihre-fc = 0
em-stepsize = 0.01
em-tol = 1000
niter = 20
fc-stepsize = 0
nstcgsteep = 1000
nbfgscorr = 10
ConstAlg = Lincs
shake-tol = 0.0001
lincs-order = 4
lincs-warnangle = 30
lincs-iter = 1
bd-fric = 0
ld-seed = 1993
cos-accel = 0
deform (3x3):
deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
adress = FALSE
userint1 = 0
userint2 = 0
userint3 = 0
userint4 = 0
userreal1 = 0
userreal2 = 0
userreal3 = 0
userreal4 = 0
grpopts:
nrdf: 95838
ref-t: 0
tau-t: 0
anneal: No
ann-npoints: 0
acc: 0 0 0
nfreeze: N N N
energygrp-flags[ 0]: 0
efield-x:
n = 0
efield-xt:
n = 0
efield-y:
n = 0
efield-yt:
n = 0
efield-z:
n = 0
efield-zt:
n = 0
bQMMM = FALSE
QMconstraints = 0
QMMMscheme = 0
scalefactor = 1
qm-opts:
ngQM = 0
Initializing Domain Decomposition on 8 nodes
Dynamic load balancing: no
Will sort the charge groups at every domain (re)decomposition
Initial maximum inter charge-group distances:
two-body bonded interactions: 6.302 nm, Bond, atoms 8476 8477
multi-body bonded interactions: 6.302 nm, Angle, atoms 8476 8477
Bonds shouldn't be 6.3 nm long. Something is wrong with your input coordinates.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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