Hello,
This problem seems to be quite common, but I still cannot solve it.
I am getting following run for mdrun
starting mdrun 'System'
100 steps, 0.0 ps.
step 0Segmentation fault: 11
If I look at md.log (full file at the end)
Grid: 3 x 3 x 2 cells
Energies (kJ/mol)
Tab. Bonds Tab. Angles LJ (SR) Coulomb (SR) Potential
3.04316e+06 2.54618e+11 7.44689e+02 -1.11165e+05 2.54621e+11
Kinetic En. Total Energy Conserved En. Temperature Pressure (bar)
1.95365e+13 1.97912e+13 1.97912e+13 *8.33224e+12*
0.00000e+00
My temperature is insanely hight. I wouldn't normally panic for the T to be
extremel high at the first step (correct?). I cannot get more insights on my
the error occurs. I could always blame it on poor minimisation, but systems
not inadequate at the start.
I am using 9-6 LJ and tabulated bonded & angle potentials.
I would be very happy to hear any advises,
Thank you
V
Full md.log:
valentina$ more md.log
Log file opened on Tue Nov 26 22:07:50 2013
Host: oparin01.earthsci.dur.ac.uk pid: 18263 nodeid: 0 nnodes: 1
Gromacs version: VERSION 4.6
Precision: single
Memory model: 64 bit
MPI library: thread_mpi
OpenMP support: disabled
GPU support: disabled
invsqrt routine: gmx_software_invsqrt(x)
CPU acceleration: AVX_256
FFT library: fftw-3.3.3
Large file support: enabled
RDTSCP usage: enabled
Built on: Wed 27 Feb 2013 12:50:27 GMT
Built by: valent...@oparin01.earthsci.dur.ac.uk [CMAKE]
Build OS/arch: Darwin 12.2.1 x86_64
Build CPU vendor: GenuineIntel
Build CPU brand: Intel(R) Core(TM) i7-3720QM CPU @ 2.60GHz
Build CPU family: 6 Model: 58 Stepping: 9
Build CPU features: aes 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 Clang Apple clang version 4.1
(tags/Apple/clang-421.11.66) (based on LLVM 3.1svn)
C compiler flags: -mavx -Wall -Wno-unused -Wunused-value
-Wno-unknown-pragmas -O3 -DNDEBUG
:-) G R O M A C S (-:
<B8><8D><9E><89><9A><93>߭<8A><9D><8C>߰<99><8B><9A><91>߲<9E><91><86><U+07FE><88><99><8A><93><93><86><U+07FC><9E><8A><8B><9A><8D><96><85><9A><9B>߬<90><8D>
<9A><8C>
:-) VERSION 4.6 (-:
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 = md
nsteps = 100
init-step = 0
cutoff-scheme = Group
ns_type = Grid
nstlist = 10
ndelta = 2
nstcomm = 100
comm-mode = Linear
nstlog = 1000
nstxout = 1
nstvout = 1
nstfout = 0
nstcalcenergy = 1
nstenergy = 1
nstxtcout = 0
init-t = 0
delta-t = 5e-05
xtcprec = 1000
fourierspacing = 0.12
nkx = 0
nky = 0
nkz = 0
pme-order = 4
ewald-rtol = 1e-05
ewald-geometry = 0
epsilon-surface = 0
optimize-fft = FALSE
ePBC = xy
bPeriodicMols = TRUE
bContinuation = FALSE
bShakeSOR = FALSE
etc = V-rescale
bPrintNHChains = FALSE
nsttcouple = 10
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 = 0.7
rlistlong = 0.7
nstcalclr = 0
rtpi = 0.05
coulombtype = User
coulomb-modifier = None
rcoulomb-switch = 0
rcoulomb = 0.7
vdwtype = User
vdw-modifier = None
rvdw-switch = 0
rvdw = 0.7
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 = 10
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: 564
ref-t: 500
tau-t: 1
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
Using 1 MPI thread
Detecting CPU-specific acceleration.
Present hardware specification:
Vendor: GenuineIntel
Brand: Intel(R) Core(TM) i7-3720QM CPU @ 2.60GHz
Family: 6 Model: 58 Stepping: 9
Features: aes 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
Acceleration most likely to fit this hardware: AVX_256
Acceleration selected at GROMACS compile time: AVX_256
Table routines are used for coulomb: TRUE
Table routines are used for vdw: TRUE
Cut-off's: NS: 0.7 Coulomb: 0.7 LJ: 0.7
System total charge: -0.000
Read user tables from table6-9.xvg with 1501 data points.
Tabscale = 500 points/nm
Read user tables from table_b0.xvg with 1001 data points.
Tabscale = 500 points/nm
Read user tables from table_b1.xvg with 1001 data points.
Tabscale = 500 points/nm
Read user tables from table_b2.xvg with 1001 data points.
Tabscale = 500 points/nm
Read user tables from table_a1.xvg with 901 data points.
Read user tables from table_a2.xvg with 901 data points.
Read user tables from table_a3.xvg with 901 data points.
Read user tables from table_a4.xvg with 901 data points.
Read user tables from table_a5.xvg with 901 data points.
Potential shift: LJ r^-12: 0.000 r^-6 0.000
Center of mass motion removal mode is Linear
We have the following groups for center of mass motion removal:
0: rest
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
G. Bussi, D. Donadio and M. Parrinello
Canonical sampling through velocity rescaling
J. Chem. Phys. 126 (2007) pp. 014101
-------- -------- --- Thank You --- -------- --------
There are: 189 Atoms
Initial temperature: 0 K
Started mdrun on node 0 Tue Nov 26 22:07:50 2013
Step Time Lambda
0 0.00000 0.00000
Grid: 3 x 3 x 2 cells
Energies (kJ/mol)
Tab. Bonds Tab. Angles LJ (SR) Coulomb (SR) Potential
3.04316e+06 2.54618e+11 7.44689e+02 -1.11165e+05 2.54621e+11
Kinetic En. Total Energy Conserved En. Temperature Pressure (bar)
1.95365e+13 1.97912e+13 1.97912e+13 8.33224e+12 0.00000e+00
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