[gmx-users] ci variable range error in parallel but NOT in serial
dtmirij
dtmirij at sandia.gov
Sat May 19 23:04:56 CEST 2007
For the two processor job:
>From my .mdp file, the pressure input data is as follows:
_________________________________________________________________________
; Pressure coupling =
Pcoupl = Berendsen
Pcoupltype = Anisotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar) =
tau_p = 1.0 1.0 1.0
compressibility = 5e-6 5e-6 5e-6 0 0 0
ref_p = 1.0 1.0 1.0 1.0 1.0 1.0
__________________________________________________________________________
The box info for the starting structure is as follows:
boxx=6.20239
boxy=6.81389
boxz=8.61949
__________________________________________________________________________
at 20504.000000 ps
boxx=5.992789
boxy=6.585367
boxz=8.999877
__________________________________________________________________________
I can't give the value of the box_lengths "right" before the crash as I
wrote out every 4 ps.
I am running a coarse grained lipid and water simulation DPPC/W
Most of the md0.log is as follows:
__________________________________________________________________________
CPU= 0, lastcg= 1517, targetcg= 3035, myshift= 1
CPU= 1, lastcg= 3035, targetcg= 1518, myshift= 1
nsb->shift = 1, nsb->bshift= 0
Listing Scalars
nsb->nodeid: 0
nsb->nnodes: 2
nsb->cgtotal: 3036
nsb->natoms: 3036
nsb->shift: 1
nsb->bshift: 0
Nodeid index homenr cgload workload
0 0 1518 1518 1518
1 1518 1518 3036 3036
parameters of the run:
integrator = md
nsteps = 1000000
init_step = 0
ns_type = Grid
nstlist = 10
ndelta = 2
bDomDecomp = FALSE
decomp_dir = 0
nstcomm = 1
comm_mode = Linear
nstcheckpoint = 1000
nstlog = 1000
nstxout = 1000
nstvout = 1000
nstfout = 0
nstenergy = 100
nstxtcout = 1000
init_t = 0
delta_t = 0.04
xtcprec = 1000
nkx = 10
nky = 10
nkz = 10
pme_order = 4
ewald_rtol = 1e-05
ewald_geometry = 0
epsilon_surface = 0
optimize_fft = FALSE
ePBC = xyz
bUncStart = FALSE
bShakeSOR = FALSE
etc = Berendsen
epc = Berendsen
epctype = Anisotropic
tau_p = 1
ref_p (3x3):
ref_p[ 0]={ 1.00000e+00, 1.00000e+00, 1.00000e+00}
ref_p[ 1]={ 1.00000e+00, 1.00000e+00, 1.00000e+00}
ref_p[ 2]={ 1.00000e+00, 1.00000e+00, 1.00000e+00}
compress (3x3):
compress[ 0]={ 5.00000e-06, 0.00000e+00, 0.00000e+00}
compress[ 1]={ 0.00000e+00, 5.00000e-06, 0.00000e+00}
compress[ 2]={ 0.00000e+00, 0.00000e+00, 5.00000e-06}
andersen_seed = 815131
rlist = 1.2
coulombtype = Shift
rcoulomb_switch = 0
rcoulomb = 1.2
vdwtype = Shift
rvdw_switch = 0.9
rvdw = 1.2
epsilon_r = 20
epsilon_rf = 1
tabext = 1
gb_algorithm = Still
nstgbradii = 1
rgbradii = 2
gb_saltconc = 0
implicit_solvent = No
DispCorr = No
fudgeQQ = 1
free_energy = no
init_lambda = 0
sc_alpha = 0
sc_power = 0
sc_sigma = 0.3
delta_lambda = 0
disre_weighting = Equal
disre_mixed = FALSE
dr_fc = 1000
dr_tau = 1.25
nstdisreout = 100
orires_fc = 0
orires_tau = 0
nstorireout = 100
dihre-fc = 1000
dihre-tau = 0
nstdihreout = 100
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}
userint1 = 0
userint2 = 0
userint3 = 0
userint4 = 0
userreal1 = 0
userreal2 = 0
userreal3 = 0
userreal4 = 0
grpopts:
nrdf: 4606.48 4498.52
ref_t: 323 323
tau_t: 1 1
anneal: No No
ann_npoints: 0 0
acc: 0 0 0
nfreeze: N N N
energygrp_flags[ 0]: 0 0
energygrp_flags[ 1]: 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
Max number of graph edges per atom is 3
Table routines are used for coulomb: TRUE
Table routines are used for vdw: TRUE
Using shifted Lennard-Jones, switch between 0.9 and 1.2 nm
Cut-off's: NS: 1.2 Coulomb: 1.2 LJ: 1.2
System total charge: 0.000
Generated table with 4400 data points for Shift.
Tabscale = 2000 points/nm
Generated table with 4400 data points for LJ6Shift.
Tabscale = 2000 points/nm
Generated table with 4400 data points for LJ12Shift.
Tabscale = 2000 points/nm
Removing pbc first time
Done rmpbc
Center of mass motion removal mode is Linear
We have the following groups for center of mass motion removal:
0: rest, initial mass: 218592
There are: 1518 Atoms
Started mdrun on node 0 Mon May 14 12:06:15 2007
Initial temperature: 0 K
Step Time Lambda
0 0.00000 0.00000
Grid: 10 x 11 x 14 cells
Configuring nonbonded kernels...
Testing x86_64 SSE2 support... present.
There are 3036 atoms in your xtc output selection
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
H. J. C. Berendsen, J. P. M. Postma, A. DiNola and J. R. Haak
Molecular dynamics with coupling to an external bath
Energies (kJ/mol)
Bond G96Angle LJ (SR) Coulomb (SR) Potential
2.53871e+03 1.06014e+03 -6.06196e+04 -2.34734e+02 -5.72555e+04
Kinetic En. Total Energy Temperature Pressure (bar)
6.91843e+02 -5.65636e+04 1.82777e+01 -3.49829e+02
Step Time Lambda
1000 40.00000 0.00000
Energies (kJ/mol)
Bond G96Angle LJ (SR) Coulomb (SR) Potential
2.12524e+03 1.11487e+03 -6.23709e+04 -2.39782e+02 -5.93705e+04
Kinetic En. Total Energy Temperature Pressure (bar)
1.21884e+04 -4.71822e+04 3.22003e+02 6.31734e+00
:
:
:
: (I won't write this all out here int he email....Dina)
:
Step Time Lambda
176000 7040.00000 0.00000
Energies (kJ/mol)
Bond G96Angle LJ (SR) Coulomb (SR) Potential
2.21615e+03 9.18647e+02 -6.24953e+04 -2.41440e+02 -5.96019e+04
Kinetic En. Total Energy Temperature Pressure (bar)
1.21050e+04 -4.74969e+04 3.19800e+02 7.30610e+01
Grid: 9 x 11 x 14 cells
Grid: 10 x 11 x 14 cells
Step Time Lambda
177000 7080.00000 0.00000
Energies (kJ/mol)
Bond G96Angle LJ (SR) Coulomb (SR) Potential
2.16313e+03 1.00661e+03 -6.26669e+04 -2.74045e+02 -5.97712e+04
Kinetic En. Total Energy Temperature Pressure (bar)
1.22833e+04 -4.74880e+04 3.24509e+02 4.51934e+01
Grid: 9 x 11 x 14 cells
Step Time Lambda
178000 7120.00000 0.00000
Energies (kJ/mol)
Bond G96Angle LJ (SR) Coulomb (SR) Potential
2.30603e+03 9.42361e+02 -6.26296e+04 -2.45039e+02 -5.96262e+04
Kinetic En. Total Energy Temperature Pressure (bar)
1.19634e+04 -4.76628e+04 3.16059e+02 7.63764e+00
Step Time Lambda
179000 7160.00000 0.00000
Energies (kJ/mol)
Bond G96Angle LJ (SR) Coulomb (SR) Potential
2.16307e+03 9.36477e+02 -6.29329e+04 -2.94713e+02 -6.01281e+04
Kinetic En. Total Energy Temperature Pressure (bar)
1.22746e+04 -4.78535e+04 3.24280e+02 -4.41846e+01
Grid: 10 x 11 x 14 cells
Grid: 9 x 11 x 14 cells
Step Time Lambda
180000 7200.00000 0.00000
Energies (kJ/mol)
Bond G96Angle LJ (SR) Coulomb (SR) Potential
2.18895e+03 9.37950e+02 -6.26262e+04 -2.71026e+02 -5.97703e+04
Kinetic En. Total Energy Temperature Pressure (bar)
1.19786e+04 -4.77917e+04 3.16462e+02 5.28903e+01
Grid: 10 x 11 x 14 cells
Grid: 9 x 11 x 14 cells
Grid: 10 x 11 x 14 cells
Grid: 9 x 11 x 14 cells
Step Time Lambda
181000 7240.00000 0.00000
Energies (kJ/mol)
Bond G96Angle LJ (SR) Coulomb (SR) Potential
2.20874e+03 9.52113e+02 -6.29877e+04 -2.27859e+02 -6.00547e+04
Kinetic En. Total Energy Temperature Pressure (bar)
1.22334e+04 -4.78213e+04 3.23192e+02 -8.78856e+00
Grid: 10 x 11 x 14 cells
Grid: 9 x 11 x 14 cells
Grid: 10 x 11 x 14 cells
Grid: 9 x 11 x 14 cells
Grid: 10 x 11 x 14 cells
Grid: 9 x 11 x 14 cells
Grid: 10 x 11 x 14 cells
Grid: 9 x 11 x 14 cells
Step Time Lambda
182000 7280.00000 0.00000
Energies (kJ/mol)
Bond G96Angle LJ (SR) Coulomb (SR) Potential
2.23314e+03 1.01388e+03 -6.29120e+04 -2.60468e+02 -5.99254e+04
Kinetic En. Total Energy Temperature Pressure (bar)
1.23519e+04 -4.75735e+04 3.26324e+02 -3.35164e-01
Grid: 10 x 11 x 14 cells
Step Time Lambda
183000 7320.00000 0.00000
Energies (kJ/mol)
Bond G96Angle LJ (SR) Coulomb (SR) Potential
2.24987e+03 1.08302e+03 -6.28072e+04 -2.29761e+02 -5.97041e+04
Kinetic En. Total Energy Temperature Pressure (bar)
1.21514e+04 -4.75526e+04 3.21027e+02 -1.87612e+01
:
:
:
:
Step Time Lambda
270000 10800.00000 0.00000
Energies (kJ/mol)
Bond G96Angle LJ (SR) Coulomb (SR) Potential
2.24564e+03 1.06224e+03 -6.25489e+04 -3.04760e+02 -5.95457e+04
Kinetic En. Total Energy Temperature Pressure (bar)
1.18952e+04 -4.76505e+04 3.14257e+02 4.90341e+01
Grid: 10 x 10 x 14 cells
Grid: 10 x 11 x 14 cells
Step Time Lambda
271000 10840.00000 0.00000
Energies (kJ/mol)
Bond G96Angle LJ (SR) Coulomb (SR) Potential
2.29629e+03 9.91349e+02 -6.27788e+04 -2.92309e+02 -5.97834e+04
Kinetic En. Total Energy Temperature Pressure (bar)
1.21229e+04 -4.76605e+04 3.20273e+02 2.23240e+01
:
:
:
:
:
Energies (kJ/mol)
Bond G96Angle LJ (SR) Coulomb (SR) Potential
2.31432e+03 9.66625e+02 -6.28789e+04 -3.20045e+02 -5.99180e+04
Kinetic En. Total Energy Temperature Pressure (bar)
1.22535e+04 -4.76645e+04 3.23724e+02 -1.21296e+01
Grid: 10 x 10 x 14 cells
Step Time Lambda
276000 11040.00000 0.00000
Energies (kJ/mol)
Bond G96Angle LJ (SR) Coulomb (SR) Potential
2.09971e+03 1.02425e+03 -6.27542e+04 -2.29513e+02 -5.98597e+04
Kinetic En. Total Energy Temperature Pressure (bar)
1.21493e+04 -4.77105e+04 3.20969e+02 5.33041e+01
:
:
:
:
Step Time Lambda
279000 11160.00000 0.00000
Energies (kJ/mol)
Bond G96Angle LJ (SR) Coulomb (SR) Potential
2.25913e+03 9.96841e+02 -6.29714e+04 -2.82496e+02 -5.99979e+04
Kinetic En. Total Energy Temperature Pressure (bar)
1.22582e+04 -4.77397e+04 3.23847e+02 5.30652e+01
Grid: 10 x 11 x 14 cells
Grid: 10 x 10 x 14 cells
Grid: 10 x 11 x 14 cells
Grid: 10 x 10 x 14 cells
Grid: 10 x 11 x 14 cells
Grid: 10 x 10 x 14 cells
Grid: 10 x 11 x 14 cells
Grid: 10 x 10 x 14 cells
Grid: 10 x 11 x 14 cells
Step Time Lambda
280000 11200.00000 0.00000
Energies (kJ/mol)
Bond G96Angle LJ (SR) Coulomb (SR) Potential
2.34614e+03 9.47004e+02 -6.26962e+04 -2.40010e+02 -5.96431e+04
Kinetic En. Total Energy Temperature Pressure (bar)
1.20579e+04 -4.75852e+04 3.18556e+02 3.15794e+01
Grid: 10 x 10 x 14 cells
Grid: 10 x 11 x 14 cells
Grid: 10 x 10 x 14 cells
Grid: 10 x 11 x 14 cells
Grid: 10 x 10 x 14 cells
Step Time Lambda
281000 11240.00000 0.00000
Energies (kJ/mol)
Bond G96Angle LJ (SR) Coulomb (SR) Potential
2.37730e+03 9.56172e+02 -6.30491e+04 -2.41021e+02 -5.99566e+04
Kinetic En. Total Energy Temperature Pressure (bar)
1.21813e+04 -4.77753e+04 3.21816e+02 -1.89902e+01
:
:
:
Step Time Lambda
455000 18200.00000 0.00000
Energies (kJ/mol)
Bond G96Angle LJ (SR) Coulomb (SR) Potential
2.28932e+03 9.33058e+02 -6.27229e+04 -2.89272e+02 -5.97898e+04
Kinetic En. Total Energy Temperature Pressure (bar)
1.20597e+04 -4.77301e+04 3.18603e+02 2.60901e+01
Grid: 10 x 11 x 14 cells
Grid: 10 x 10 x 14 cells
Grid: 10 x 11 x 14 cells
Grid: 10 x 10 x 14 cells
Step Time Lambda
456000 18240.00000 0.00000
Energies (kJ/mol)
Bond G96Angle LJ (SR) Coulomb (SR) Potential
2.23498e+03 9.68897e+02 -6.28950e+04 -2.13690e+02 -5.99048e+04
Kinetic En. Total Energy Temperature Pressure (bar)
1.21184e+04 -4.77864e+04 3.20154e+02 -7.01858e-01
Step Time Lambda
457000 18280.00000 0.00000
Energies (kJ/mol)
Bond G96Angle LJ (SR) Coulomb (SR) Potential
2.27808e+03 1.07909e+03 -6.30733e+04 -2.47294e+02 -5.99635e+04
Kinetic En. Total Energy Temperature Pressure (bar)
1.22863e+04 -4.76772e+04 3.24589e+02 -9.60393e+01
Grid: 10 x 11 x 14 cells
Step Time Lambda
458000 18320.00000 0.00000
Energies (kJ/mol)
Bond G96Angle LJ (SR) Coulomb (SR) Potential
2.32733e+03 1.03832e+03 -6.29550e+04 -2.14944e+02 -5.98043e+04
Kinetic En. Total Energy Temperature Pressure (bar)
1.22202e+04 -4.75841e+04 3.22843e+02 -1.31042e+01
Grid: 10 x 10 x 14 cells
Step Time Lambda
459000 18360.00000 0.00000
Energies (kJ/mol)
Bond G96Angle LJ (SR) Coulomb (SR) Potential
2.36226e+03 9.90104e+02 -6.31263e+04 -2.80498e+02 -6.00544e+04
Kinetic En. Total Energy Temperature Pressure (bar)
1.22247e+04 -4.78297e+04 3.22963e+02 -3.17254e+01
Grid: 10 x 11 x 14 cells
Grid: 10 x 10 x 14 cells
Step Time Lambda
460000 18400.00000 0.00000
Energies (kJ/mol)
Bond G96Angle LJ (SR) Coulomb (SR) Potential
2.38791e+03 1.07181e+03 -6.28941e+04 -2.47039e+02 -5.96815e+04
Kinetic En. Total Energy Temperature Pressure (bar)
1.20473e+04 -4.76341e+04 3.18276e+02 -2.41392e+00
Step Time Lambda
461000 18440.00000 0.00000
Energies (kJ/mol)
Bond G96Angle LJ (SR) Coulomb (SR) Potential
2.19108e+03 1.00389e+03 -6.28997e+04 -2.92142e+02 -5.99969e+04
Kinetic En. Total Energy Temperature Pressure (bar)
1.21293e+04 -4.78676e+04 3.20442e+02 3.96037e+00
Grid: 10 x 11 x 14 cells
Step Time Lambda
462000 18480.00000 0.00000
Energies (kJ/mol)
Bond G96Angle LJ (SR) Coulomb (SR) Potential
2.31548e+03 1.03984e+03 -6.28162e+04 -2.70353e+02 -5.97312e+04
Kinetic En. Total Energy Temperature Pressure (bar)
1.20583e+04 -4.76730e+04 3.18565e+02 4.88523e+00
Grid: 10 x 10 x 14 cells
Grid: 10 x 11 x 14 cells
Grid: 10 x 10 x 14 cells
Grid: 10 x 11 x 14 cells
Grid: 10 x 10 x 14 cells
Step Time Lambda
463000 18520.00000 0.00000
Energies (kJ/mol)
Bond G96Angle LJ (SR) Coulomb (SR) Potential
2.25299e+03 1.07274e+03 -6.26810e+04 -2.74113e+02 -5.96294e+04
Kinetic En. Total Energy Temperature Pressure (bar)
1.20391e+04 -4.75902e+04 3.18059e+02 3.69033e+01
Step Time Lambda
464000 18560.00000 0.00000
Energies (kJ/mol)
Bond G96Angle LJ (SR) Coulomb (SR) Potential
2.21038e+03 1.03137e+03 -6.25614e+04 -2.83521e+02 -5.96031e+04
Kinetic En. Total Energy Temperature Pressure (bar)
1.21075e+04 -4.74957e+04 3.19865e+02 6.00703e+01
Grid: 10 x 11 x 14 cells
Grid: 10 x 10 x 14 cells
Grid: 10 x 11 x 14 cells
Grid: 10 x 10 x 14 cells
Grid: 10 x 11 x 14 cells
Grid: 10 x 10 x 14 cells
Grid: 10 x 11 x 14 cells
Grid: 10 x 10 x 14 cells
Step Time Lambda
465000 18600.00000 0.00000
Energies (kJ/mol)
Bond G96Angle LJ (SR) Coulomb (SR) Potential
2.29947e+03 1.07058e+03 -6.27088e+04 -2.42785e+02 -5.95815e+04
Kinetic En. Total Energy Temperature Pressure (bar)
1.20806e+04 -4.75009e+04 3.19154e+02 -2.14849e+01
Step Time Lambda
466000 18640.00000 0.00000
Energies (kJ/mol)
Bond G96Angle LJ (SR) Coulomb (SR) Potential
2.28449e+03 1.05348e+03 -6.26540e+04 -2.42043e+02 -5.95581e+04
Kinetic En. Total Energy Temperature Pressure (bar)
1.21343e+04 -4.74238e+04 3.20575e+02 1.07024e+01
Grid: 10 x 11 x 14 cells
Grid: 10 x 10 x 14 cells
Step Time Lambda
467000 18680.00000 0.00000
Energies (kJ/mol)
Bond G96Angle LJ (SR) Coulomb (SR) Potential
2.30015e+03 1.00386e+03 -6.30087e+04 -2.79270e+02 -5.99840e+04
Kinetic En. Total Energy Temperature Pressure (bar)
1.23743e+04 -4.76097e+04 3.26915e+02 -7.45890e+01
:
:
:
Step Time Lambda
472000 18880.00000 0.00000
Energies (kJ/mol)
Bond G96Angle LJ (SR) Coulomb (SR) Potential
2.33619e+03 9.59553e+02 -6.29272e+04 -2.21953e+02 -5.98534e+04
Kinetic En. Total Energy Temperature Pressure (bar)
1.21870e+04 -4.76664e+04 3.21965e+02 -3.61315e+01
Grid: 10 x 11 x 14 cells
Grid: 10 x 10 x 14 cells
Grid: 10 x 11 x 14 cells
Grid: 10 x 10 x 14 cells
Grid: 10 x 11 x 14 cells
Grid: 10 x 10 x 14 cells
Step Time Lambda
473000 18920.00000 0.00000
Grid: 10 x 11 x 14 cells
Energies (kJ/mol)
Bond G96Angle LJ (SR) Coulomb (SR) Potential
2.26291e+03 9.88810e+02 -6.28277e+04 -2.38586e+02 -5.98146e+04
Kinetic En. Total Energy Temperature Pressure (bar)
1.20915e+04 -4.77231e+04 3.19443e+02 3.90219e+01
Grid: 10 x 10 x 14 cells
Grid: 10 x 11 x 14 cells
Grid: 10 x 10 x 14 cells
Grid: 10 x 11 x 14 cells
Grid: 10 x 10 x 14 cells
Grid: 10 x 11 x 14 cells
Grid: 10 x 10 x 14 cells
Grid: 10 x 11 x 14 cells
Step Time Lambda
474000 18960.00000 0.00000
Energies (kJ/mol)
Bond G96Angle LJ (SR) Coulomb (SR) Potential
2.26225e+03 9.81347e+02 -6.28376e+04 -2.59880e+02 -5.98539e+04
Kinetic En. Total Energy Temperature Pressure (bar)
1.21443e+04 -4.77096e+04 3.20838e+02 2.48308e+00
Grid: 10 x 10 x 14 cells
Grid: 10 x 11 x 14 cells
Grid: 10 x 10 x 14 cells
Step Time Lambda
475000 19000.00000 0.00000
Energies (kJ/mol)
Bond G96Angle LJ (SR) Coulomb (SR) Potential
2.12734e+03 9.40256e+02 -6.24442e+04 -2.79733e+02 -5.96563e+04
Kinetic En. Total Energy Temperature Pressure (bar)
1.20758e+04 -4.75804e+04 3.19030e+02 6.61082e+01
Grid: 10 x 11 x 14 cells
Step Time Lambda
476000 19040.00000 0.00000
Energies (kJ/mol)
Bond G96Angle LJ (SR) Coulomb (SR) Potential
2.15412e+03 1.00220e+03 -6.25613e+04 -2.63090e+02 -5.96681e+04
Kinetic En. Total Energy Temperature Pressure (bar)
1.20733e+04 -4.75948e+04 3.18962e+02 7.68142e+01
Grid: 10 x 10 x 14 cells
Step Time Lambda
477000 19080.00000 0.00000
Energies (kJ/mol)
Bond G96Angle LJ (SR) Coulomb (SR) Potential
2.12027e+03 9.64698e+02 -6.29191e+04 -2.62767e+02 -6.00969e+04
Kinetic En. Total Energy Temperature Pressure (bar)
1.23448e+04 -4.77521e+04 3.26135e+02 9.87805e+00
Grid: 10 x 11 x 14 cells
Grid: 10 x 10 x 14 cells
Grid: 10 x 11 x 14 cells
Grid: 10 x 10 x 14 cells
Grid: 10 x 11 x 14 cells
Step Time Lambda
478000 19120.00000 0.00000
Energies (kJ/mol)
Bond G96Angle LJ (SR) Coulomb (SR) Potential
2.37971e+03 9.93991e+02 -6.26914e+04 -2.73074e+02 -5.95907e+04
Kinetic En. Total Energy Temperature Pressure (bar)
1.20501e+04 -4.75406e+04 3.18349e+02 2.22324e+01
:
:
:
Step Time Lambda
486000 19440.00000 0.00000
Energies (kJ/mol)
Bond G96Angle LJ (SR) Coulomb (SR) Potential
2.25999e+03 9.88818e+02 -6.28026e+04 -2.41107e+02 -5.97949e+04
Kinetic En. Total Energy Temperature Pressure (bar)
1.21510e+04 -4.76439e+04 3.21016e+02 -4.84147e+00
Grid: 9 x 11 x 14 cells
Step Time Lambda
487000 19480.00000 0.00000
Energies (kJ/mol)
Bond G96Angle LJ (SR) Coulomb (SR) Potential
2.28673e+03 9.43517e+02 -6.28426e+04 -2.60572e+02 -5.98729e+04
Kinetic En. Total Energy Temperature Pressure (bar)
1.21760e+04 -4.76969e+04 3.21676e+02 1.23444e+01
Grid: 10 x 11 x 14 cells
Grid: 9 x 11 x 14 cells
Grid: 10 x 11 x 14 cells
Step Time Lambda
488000 19520.00000 0.00000
Energies (kJ/mol)
Bond G96Angle LJ (SR) Coulomb (SR) Potential
2.09429e+03 9.98686e+02 -6.28032e+04 -2.62685e+02 -5.99730e+04
Kinetic En. Total Energy Temperature Pressure (bar)
1.22589e+04 -4.77140e+04 3.23866e+02 4.78195e+01
Grid: 9 x 11 x 14 cells
Grid: 10 x 11 x 14 cells
Grid: 9 x 11 x 14 cells
Grid: 10 x 11 x 14 cells
Grid: 9 x 11 x 14 cells
Grid: 10 x 11 x 14 cells
Grid: 9 x 11 x 14 cells
Step Time Lambda
489000 19560.00000 0.00000
Energies (kJ/mol)
Bond G96Angle LJ (SR) Coulomb (SR) Potential
2.31226e+03 9.97728e+02 -6.28567e+04 -2.06873e+02 -5.97536e+04
Kinetic En. Total Energy Temperature Pressure (bar)
1.21375e+04 -4.76161e+04 3.20658e+02 -2.45940e+01
Grid: 10 x 11 x 14 cells
Step Time Lambda
490000 19600.00000 0.00000
Energies (kJ/mol)
Bond G96Angle LJ (SR) Coulomb (SR) Potential
2.36548e+03 9.28537e+02 -6.27370e+04 -2.35436e+02 -5.96784e+04
Kinetic En. Total Energy Temperature Pressure (bar)
1.21506e+04 -4.75278e+04 3.21004e+02 7.47262e+00
Grid: 9 x 11 x 14 cells
Step Time Lambda
491000 19640.00000 0.00000
Energies (kJ/mol)
Bond G96Angle LJ (SR) Coulomb (SR) Potential
2.29913e+03 1.00172e+03 -6.29838e+04 -2.57971e+02 -5.99409e+04
Kinetic En. Total Energy Temperature Pressure (bar)
1.21964e+04 -4.77445e+04 3.22215e+02 -3.52855e+01
Grid: 10 x 11 x 14 cells
Grid: 9 x 11 x 14 cells
Grid: 10 x 11 x 14 cells
Grid: 9 x 11 x 14 cells
Grid: 10 x 11 x 14 cells
Step Time Lambda
492000 19680.00000 0.00000
Energies (kJ/mol)
Bond G96Angle LJ (SR) Coulomb (SR) Potential
2.26688e+03 1.04259e+03 -6.28482e+04 -2.32373e+02 -5.97711e+04
Kinetic En. Total Energy Temperature Pressure (bar)
1.21568e+04 -4.76143e+04 3.21168e+02 -1.76854e+01
Grid: 9 x 11 x 14 cells
Grid: 10 x 11 x 14 cells
Step Time Lambda
493000 19720.00000 0.00000
Energies (kJ/mol)
Bond G96Angle LJ (SR) Coulomb (SR) Potential
2.24526e+03 1.02109e+03 -6.28704e+04 -2.27131e+02 -5.98312e+04
Kinetic En. Total Energy Temperature Pressure (bar)
1.21612e+04 -4.76700e+04 3.21285e+02 -1.95963e+00
:
:
:
Step Time Lambda
496000 19840.00000 0.00000
Energies (kJ/mol)
Bond G96Angle LJ (SR) Coulomb (SR) Potential
2.14140e+03 9.49850e+02 -6.27336e+04 -2.75620e+02 -5.99179e+04
Kinetic En. Total Energy Temperature Pressure (bar)
1.21765e+04 -4.77415e+04 3.21688e+02 4.02447e+01
Grid: 9 x 11 x 14 cells
Grid: 10 x 11 x 14 cells
Grid: 9 x 11 x 14 cells
Grid: 10 x 11 x 14 cells
Step Time Lambda
497000 19880.00000 0.00000
Energies (kJ/mol)
Bond G96Angle LJ (SR) Coulomb (SR) Potential
2.26808e+03 9.77544e+02 -6.29488e+04 -2.43013e+02 -5.99462e+04
Kinetic En. Total Energy Temperature Pressure (bar)
1.22133e+04 -4.77329e+04 3.22661e+02 -3.92715e+01
Grid: 9 x 11 x 14 cells
Grid: 10 x 11 x 14 cells
Grid: 9 x 11 x 14 cells
Grid: 10 x 11 x 14 cells
Step Time Lambda
498000 19920.00000 0.00000
Energies (kJ/mol)
Bond G96Angle LJ (SR) Coulomb (SR) Potential
2.21031e+03 9.09740e+02 -6.26993e+04 -2.65471e+02 -5.98447e+04
Kinetic En. Total Energy Temperature Pressure (bar)
1.22178e+04 -4.76269e+04 3.22779e+02 1.72754e+01
Grid: 9 x 11 x 14 cells
Grid: 10 x 11 x 14 cells
Grid: 9 x 11 x 14 cells
Grid: 10 x 11 x 14 cells
Step Time Lambda
499000 19960.00000 0.00000
Energies (kJ/mol)
Bond G96Angle LJ (SR) Coulomb (SR) Potential
2.25159e+03 9.57672e+02 -6.31363e+04 -2.61455e+02 -6.01885e+04
Kinetic En. Total Energy Temperature Pressure (bar)
1.23944e+04 -4.77941e+04 3.27445e+02 -5.31052e+01
Grid: 9 x 11 x 14 cells
Step Time Lambda
500000 20000.00000 0.00000
Energies (kJ/mol)
Bond G96Angle LJ (SR) Coulomb (SR) Potential
2.36375e+03 9.34406e+02 -6.27648e+04 -2.71641e+02 -5.97383e+04
Kinetic En. Total Energy Temperature Pressure (bar)
1.20291e+04 -4.77092e+04 3.17795e+02 2.23045e+01
Grid: 10 x 11 x 14 cells
Step Time Lambda
501000 20040.00000 0.00000
Energies (kJ/mol)
Bond G96Angle LJ (SR) Coulomb (SR) Potential
2.24554e+03 9.80450e+02 -6.26002e+04 -2.96703e+02 -5.96709e+04
Kinetic En. Total Energy Temperature Pressure (bar)
1.21105e+04 -4.75604e+04 3.19945e+02 4.23439e+01
Step Time Lambda
502000 20080.00000 0.00000
Energies (kJ/mol)
Bond G96Angle LJ (SR) Coulomb (SR) Potential
2.31243e+03 9.42869e+02 -6.25208e+04 -2.49302e+02 -5.95148e+04
Kinetic En. Total Energy Temperature Pressure (bar)
1.20395e+04 -4.74753e+04 3.18070e+02 1.62679e+01
Step Time Lambda
503000 20120.00000 0.00000
Energies (kJ/mol)
Bond G96Angle LJ (SR) Coulomb (SR) Potential
2.27867e+03 9.91391e+02 -6.27577e+04 -2.26733e+02 -5.97144e+04
Kinetic En. Total Energy Temperature Pressure (bar)
1.21483e+04 -4.75661e+04 3.20942e+02 9.03223e+00
Grid: 10 x 10 x 14 cells
Step Time Lambda
504000 20160.00000 0.00000
Energies (kJ/mol)
Bond G96Angle LJ (SR) Coulomb (SR) Potential
2.16771e+03 9.33599e+02 -6.28007e+04 -2.19292e+02 -5.99186e+04
Kinetic En. Total Energy Temperature Pressure (bar)
1.21352e+04 -4.77835e+04 3.20597e+02 7.06729e+01
Grid: 10 x 11 x 14 cells
Grid: 10 x 10 x 14 cells
Grid: 10 x 11 x 14 cells
Grid: 10 x 10 x 14 cells
Grid: 10 x 11 x 14 cells
Grid: 10 x 10 x 14 cells
Grid: 10 x 11 x 14 cells
Grid: 10 x 10 x 14 cells
Grid: 10 x 11 x 14 cells
Grid: 10 x 10 x 14 cells
Step Time Lambda
505000 20200.00000 0.00000
Energies (kJ/mol)
Bond G96Angle LJ (SR) Coulomb (SR) Potential
2.27809e+03 1.01425e+03 -6.29092e+04 -2.91546e+02 -5.99084e+04
Kinetic En. Total Energy Temperature Pressure (bar)
1.20702e+04 -4.78382e+04 3.18881e+02 -9.06578e+00
Grid: 10 x 11 x 14 cells
Step Time Lambda
506000 20240.00000 0.00000
Energies (kJ/mol)
Bond G96Angle LJ (SR) Coulomb (SR) Potential
2.15380e+03 1.03106e+03 -6.27440e+04 -3.02653e+02 -5.98618e+04
Kinetic En. Total Energy Temperature Pressure (bar)
1.21376e+04 -4.77242e+04 3.20662e+02 2.05705e+01
Grid: 10 x 10 x 14 cells
Step Time Lambda
507000 20280.00000 0.00000
Energies (kJ/mol)
Bond G96Angle LJ (SR) Coulomb (SR) Potential
2.13626e+03 1.05216e+03 -6.27805e+04 -2.65303e+02 -5.98574e+04
Kinetic En. Total Energy Temperature Pressure (bar)
1.21935e+04 -4.76640e+04 3.22137e+02 -6.81582e+00
Grid: 10 x 11 x 14 cells
Grid: 10 x 10 x 14 cells
Grid: 10 x 11 x 14 cells
Grid: 10 x 10 x 14 cells
Step Time Lambda
508000 20320.00000 0.00000
Energies (kJ/mol)
Bond G96Angle LJ (SR) Coulomb (SR) Potential
2.33777e+03 9.37635e+02 -6.30120e+04 -2.60291e+02 -5.99969e+04
Kinetic En. Total Energy Temperature Pressure (bar)
1.22535e+04 -4.77434e+04 3.23723e+02 -7.24406e+01
Step Time Lambda
510000 20400.00000 0.00000
Energies (kJ/mol)
Bond G96Angle LJ (SR) Coulomb (SR) Potential
2.22685e+03 9.91703e+02 -6.27863e+04 -3.06843e+02 -5.98745e+04
Kinetic En. Total Energy Temperature Pressure (bar)
1.20990e+04 -4.77755e+04 3.19642e+02 -5.28281e+00
Grid: 9 x 10 x 14 cells
Grid: 10 x 10 x 14 cells
Grid: 9 x 10 x 14 cells
Step Time Lambda
511000 20440.00000 0.00000
Energies (kJ/mol)
Bond G96Angle LJ (SR) Coulomb (SR) Potential
2.28256e+03 1.05281e+03 -6.30340e+04 -2.59348e+02 -5.99579e+04
Kinetic En. Total Energy Temperature Pressure (bar)
1.21040e+04 -4.78539e+04 3.19773e+02 9.89601e-01
Step Time Lambda
512000 20480.00000 0.00000
Energies (kJ/mol)
Bond G96Angle LJ (SR) Coulomb (SR) Potential
2.31161e+03 1.00891e+03 -6.29750e+04 -2.63548e+02 -5.99180e+04
Kinetic En. Total Energy Temperature Pressure (bar)
1.22244e+04 -4.76936e+04 3.22953e+02 -8.72543e+00
Grid: 9 x 10 x 15 cells
Grid: 9 x 10 x 14 cells
Grid: 9 x 10 x 15 cells
Grid: 9 x 10 x 14 cells
Grid: 9 x 10 x 15 cells
Grid: 9 x 10 x 14 cells
Grid: 9 x 10 x 15 cells
Grid: 9 x 10 x 14 cells
Grid: 9 x 10 x 15 cells
Grid: 9 x 10 x 14 cells
Grid: 9 x 10 x 15 cells
Step Time Lambda
513000 20520.00000 0.00000
Energies (kJ/mol)
Bond G96Angle LJ (SR) Coulomb (SR) Potential
2.27041e+03 9.29009e+02 -6.27536e+04 -2.41948e+02 -5.97961e+04
Kinetic En. Total Energy Temperature Pressure (bar)
1.20568e+04 -4.77393e+04 3.18526e+02 2.50364e+01
Step Time Lambda
514000 20560.00000 0.00000
Energies (kJ/mol)
Bond G96Angle LJ (SR) Coulomb (SR) Potential
2.35814e+03 9.72124e+02 -6.27263e+04 -2.80627e+02 -5.96767e+04
Kinetic En. Total Energy Temperature Pressure (bar)
1.20707e+04 -4.76060e+04 3.18893e+02 3.46136e+01
Step Time Lambda
515000 20600.00000 0.00000
Energies (kJ/mol)
Bond G96Angle LJ (SR) Coulomb (SR) Potential
2.35990e+03 9.68742e+02 -6.27853e+04 -2.78126e+02 -5.97348e+04
Kinetic En. Total Energy Temperature Pressure (bar)
1.20672e+04 -4.76677e+04 3.18800e+02 2.96154e+01
Step Time Lambda
516000 20640.00000 0.00000
Energies (kJ/mol)
Bond G96Angle LJ (SR) Coulomb (SR) Potential
2.18823e+03 9.64202e+02 -6.27980e+04 -2.71796e+02 -5.99173e+04
Kinetic En. Total Energy Temperature Pressure (bar)
1.21154e+04 -4.78019e+04 3.20074e+02 6.12343e+01
Step Time Lambda
517000 20680.00000 0.00000
Energies (kJ/mol)
Bond G96Angle LJ (SR) Coulomb (SR) Potential
2.25203e+03 9.73365e+02 -6.29358e+04 -2.95630e+02 -6.00060e+04
Kinetic En. Total Energy Temperature Pressure (bar)
1.22062e+04 -4.77998e+04 3.22474e+02 6.28677e+00
Grid: 9 x 11 x 15 cells
Grid: 9 x 10 x 15 cells
Grid: 9 x 11 x 15 cells
Grid: 9 x 10 x 15 cells
Grid: 9 x 11 x 15 cells
Step Time Lambda
518000 20720.00000 0.00000
Energies (kJ/mol)
Bond G96Angle LJ (SR) Coulomb (SR) Potential
2.23215e+03 1.04959e+03 -6.26156e+04 -2.47699e+02 -5.95815e+04
Kinetic En. Total Energy Temperature Pressure (bar)
1.20679e+04 -4.75137e+04 3.18818e+02 7.69231e+01
Step Time Lambda
519000 20760.00000 0.00000
Energies (kJ/mol)
Bond G96Angle LJ (SR) Coulomb (SR) Potential
2.30392e+03 1.08218e+03 -6.29069e+04 -2.11517e+02 -5.97323e+04
Kinetic En. Total Energy Temperature Pressure (bar)
1.21468e+04 -4.75856e+04 3.20903e+02 -1.67980e+01
Grid: 9 x 11 x 14 cells
-------------------------------------------------------
Program mdrun_d_p, VERSION 3.3.1
Source code file: nsgrid.c, line: 226
Range checking error:
Explanation: During neighborsearching, we assign each particle to a grid
based on its coordinates. If your system contains collisions or parameter
errors that give particles very high velocities you might end up with some
coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
put these on a grid, so this is usually where we detect those errors.
Make sure your system is properly energy-minimized and that the potential
energy seems reasonable before trying again.
Variable ci has value 1434. It should have been within [ 0 .. 1386 ]
Please report this to the mailing list (gmx-users at gromacs.org)
-------------------------------------------------------
"Do You Have a Mind of Your Own ?" (Garbage)
-------------------------------------------------------
-------------------------------------------------------
-------------------------------------------------------
the md1.log is as follows:
-------------------------------------------------------
Log file opened on Mon May 14 12:06:14 2007
Host: an173 pid: 18497 nodeid: 1 nnodes: 2
The Gromacs distribution was built Tue Apr 24 18:29:43 MDT 2007 by
dtmirij at alogin1.sandia.gov (Linux 2.6.9-42.0.2.EL_lustre.1.4.7.3smp x86_64)
Max number of graph edges per atom is 3
Table routines are used for coulomb: TRUE
Table routines are used for vdw: TRUE
Using shifted Lennard-Jones, switch between 0.9 and 1.2 nm
Cut-off's: NS: 1.2 Coulomb: 1.2 LJ: 1.2
System total charge: 0.000
Generated table with 4400 data points for Shift.
Tabscale = 2000 points/nm
Generated table with 4400 data points for LJ6Shift.
Tabscale = 2000 points/nm
Generated table with 4400 data points for LJ12Shift.
Tabscale = 2000 points/nm
Removing pbc first time
Done rmpbc
Center of mass motion removal mode is Linear
We have the following groups for center of mass motion removal:
0: rest, initial mass: 218592
There are: 1518 Atoms
Started mdrun on node 1 Mon May 14 12:06:15 2007
Grid: 10 x 11 x 14 cells
Configuring nonbonded kernels...
Testing x86_64 SSE2 support... present.
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
H. J. C. Berendsen, J. P. M. Postma, A. DiNola and J. R. Haak
Molecular dynamics with coupling to an external bath
J. Chem. Phys. 81 (1984) pp. 3684-3690
-------- -------- --- Thank You --- -------- --------
-------------------------------------------------------
-------------------------------------------------------
-Dina
On 5/19/07 2:15 PM, "David van der Spoel" <spoel at xray.bmc.uu.se> wrote:
> dtmirij wrote:
>> Mark,
>> That was a typo in the second paragraph.
>> I meant:
>> " When I run the exact same system from the same starting conditions using
>> my PARALLEL built executable on two processors, I get the following error
>> after running for over a half million timesteps"
>>
>> And by the way this error will happen after different ps of simulation from
>> starting conditions when I use different number of processor (obviously as
>> the trajectories will be different).
>>
>> And each time the ci value is just "barely" out of range. I saw in another
>> posting about this ci problem that it could have to do with the pressure
>> coupling..
>>
>> Any suggestions
>>
> Yes, give us more data: pressure coupling input, box just before the
> crash, original box and so on.
>
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