Hi,
My simulation has fall over with this error:
t = 501.346 ps: Water molecule starting at atom 8367 can not be settled.
Check for bad contacts and/or reduce the timestep.Wrote pdb files
with previous
and current coordinates
What can I do to fix it? There are a few other that have had this
problem on the list, but none are using 3.3.3 or have posted the
solution.
Bryn
-------- -------- --- Thank You --- -------- --------
Input Parameters:
integrator = md
nsteps = 25000000
init_step = 0
ns_type = Grid
nstlist = 10
ndelta = 2
bDomDecomp = FALSE
decomp_dir = 0
nstcomm = 1
comm_mode = Linear
nstcheckpoint = 1000
nstlog = 100
nstxout = 100000
nstvout = 100000
nstfout = 0
nstenergy = 1000
nstxtcout = 1000
init_t = 0
delta_t = 0.002
xtcprec = 1000
nkx = 39
nky = 39
nkz = 39
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 = No
epctype = Isotropic
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}
andersen_seed = 815131
rlist = 1
coulombtype = PME
rcoulomb_switch = 0
rcoulomb = 1
vdwtype = Cut-off
rvdw_switch = 0
rvdw = 1
epsilon_r = 1
epsilon_rf = 1
tabext = 1
gb_algorithm = Still
nstgbradii = 1
rgbradii = 2
gb_saltconc = 0
implicit_solvent = No
DispCorr = No
fudgeQQ = 0.8333
free_energy = no
init_lambda = 0
sc_alpha = 0
sc_power = 0
sc_sigma = 0.3
delta_lambda = 0
disre_weighting = Conservative
disre_mixed = FALSE
dr_fc = 1000
dr_tau = 0
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 = 1e-04
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: 2585.45 11571.5
ref_t: 298 298
tau_t: 0.1 0.1
anneal: No No
ann_npoints: 0 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
CPU= 0, lastcg= 2789, targetcg= 1394, myshift= 0
nsb->shift = 1, nsb->bshift= 0
Neighbor Search Blocks
nsb->nodeid: 0
nsb->nnodes: 1
nsb->cgtotal: 2790
nsb->natoms: 8576
nsb->shift: 1
nsb->bshift: 0
Nodeid index homenr cgload workload
0 0 8576 2790 2790
Max number of connections per atom is 58
Total number of connections is 34155
Max number of graph edges per atom is 4
Total number of graph edges is 13304
Table routines are used for coulomb: TRUE
Table routines are used for vdw: FALSE
Using a Gaussian width (1/beta) of 0.320163 nm for Ewald
Cut-off's: NS: 1 Coulomb: 1 LJ: 1
System total charge: -0.000
Generated table with 1000 data points for Ewald.
Tabscale = 500 points/nm
Generated table with 1000 data points for LJ6.
Tabscale = 500 points/nm
Generated table with 1000 data points for LJ12.
Tabscale = 500 points/nm
Generated table with 500 data points for 1-4 COUL.
Tabscale = 500 points/nm
Generated table with 500 data points for 1-4 LJ6.
Tabscale = 500 points/nm
Generated table with 500 data points for 1-4 LJ12.
Tabscale = 500 points/nm
Will do PME sum in reciprocal space.
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
U. Essman, L. Perela, M. L. Berkowitz, T. Darden, H. Lee and L. G.
Pedersen
A smooth particle mesh Ewald method
J. Chem. Phys. 103 (1995) pp. 8577-8592
-------- -------- --- Thank You --- -------- --------
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: 40986
There are: 6648 Atoms
There are: 1928 VSites
Constraining the starting coordinates (step -2)
++++ 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 --- -------- --------
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
S. Miyamoto and P. A. Kollman
SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for
Rigid
Water Models
J. Comp. Chem. 13 (1992) pp. 952-962
-------- -------- --- Thank You --- -------- --------
Going to use C-settle (1928 waters)
wo = 0.888099, wh =0.0559503, wohh = 18.016, rc = 0.075695, ra =
0.00655606
rb = 0.0520322, rc2 = 0.15139, rone = 1, dHH = 0.15139, dOH = 0.09572
Constraining the coordinates at t0-dt (step -1)
Started mdrun on node 0 Mon May 19 20:45:24 2008
Initial temperature: 297.366 K
Step Time Lambda
0 0.00000 0.00000
Grid: 9 x 9 x 6 cells
Configuring nonbonded kernels...
Testing ia64 CPU family...Unknown Itanium
You might want to test the speed without assembly kernels
by setting the NOASSEMBLYLOOPS environment variable.
Using single precision ia64 assembly kernels.
There are 8576 atoms in your xtc output selection
Energies (kJ/mol)
Bond Angle Proper Dih. Ryckaert-
Bell. LJ-14
1.16658e+03 1.50951e+03 1.16314e+02 2.20836e+03
8.53452e+02
Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip.
Potential
1.26649e+04 1.46610e+04 -1.05763e+05 -2.44216e+04
-9.70041e+04
Kinetic En. Total Energy Temperature Pressure (bar)
1.75575e+04 -7.94466e+04 2.98322e+02 -3.03702e+02
Step Time Lambda
100 0.20000 0.00000
Energies (kJ/mol)
Bond Angle Proper Dih. Ryckaert-
Bell. LJ-14
1.24614e+03 1.69712e+03 8.82866e+01 2.23098e+03
7.82338e+02
Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip.
Potential
1.25864e+04 1.44700e+04 -1.05455e+05 -2.44167e+04
-9.67700e+04
Kinetic En. Total Energy Temperature Pressure (bar)
1.74988e+04 -7.92712e+04 2.97324e+02 -5.65797e+02
...
Step Time Lambda
250600 501.20001 0.00000
Energies (kJ/mol)
Bond Angle Proper Dih. Ryckaert-
Bell. LJ-14
9.86208e+03 1.76614e+03 8.61447e+01 2.12415e+03
7.68211e+02
Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip.
Potential
1.27013e+04 1.47187e+04 -1.05739e+05 -2.44341e+04
-8.81461e+04
Kinetic En. Total Energy Temperature Pressure (bar)
2.34873e+04 -6.46589e+04 3.99075e+02 -1.90442e+03
t = 501.346 ps: Water molecule starting at atom 8367 can not be settled.
Check for bad contacts and/or reduce the timestep.Wrote pdb files
with previous
and current coordinates
===========================================================
R. Bryn Fenwick Department of Biochemistry,
rbf22atcam.ac.uk University of Cambridge,
bryn.fenwickatcantab.net 80 Tennis Court Road,
Tel: +44 1223 766018 Old Addenbrookes Site,
Fax: +44 1223 766002 Cambridge, CB2 1GA, UK.
===========================================================
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