[gmx-users] Range Checking Error
Gaurav Chopra
gauravc at stanford.edu
Tue Mar 14 15:17:24 CET 2006
/ />/
/>/ />/ 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.
/>/ /Please follow the advice in the above two sentences. Check your structure.
/>/
/>/ I did the energy minimization by increasing the number of steps using steepest descent, nothing happened. Then I tried cg using -DFLEXIBLE
/>/ and steep using -DFLEXIBLE in my mdp file and I was able to compute using mdrun but I got the following in my log file
/>/
/>/ Initiating Steepest Descents
/>/ Center of mass motion removal mode is Linear
/>/ We have the following groups for center of mass motion removal:
/>/ 0: rest, initial mass: 24594
/>/ Started Steepest Descents on node 0 Mon Mar 13 17:07:04 2006
/>/ Removing pbc first time
/>/ Done rmpbc
/>/ Steepest Descents:
/>/ Tolerance (Fmax) = 1.00000e+01
/>/ Number of steps = 10000
/>/ Grid: 10 x 10 x 20 cells
/>/ Configuring nonbonded kernels...
/>/ Testing AMD 3DNow support... not present.
/>/ Testing ia32 SSE support... present.
/>/
/>/
/>/ Then with this when I do position restrained md, using -DPOSRES in mdp file for grompp and md integrator and then mdrun for position restrained
/>/ I get the following
/>/
/>/ Step 0, time 0 (ps) LINCS WARNING
/>/ relative constraint deviation after LINCS:
/>/ max 1391229833052160.000000 (between atoms 655 and 657) rms 40665803128832.000000
/>/ bonds that rotated more than 30 degrees:
/
turn off the constraints
>
Hi David
I did turn off the constraints and also made the starting structure
unconstarined in the mdp file. The mdrun for position restrained gives
Segmentation fault and the log file is shown below.
Could you please suggest what could I do. I attached a pdb file in the
earlier mail which has to be reviewed by the moderator of gmx list.
Thanks
Gaurav
-------------------------------------------
Input Parameters:
integrator = md
nsteps = 1000
init_step = 0
ns_type = Grid
nstlist = 10
ndelta = 2
bDomDecomp = FALSE
decomp_dir = 0
nstcomm = 1
comm_mode = Linear
nstcheckpoint = 1000
nstlog = 10000
nstxout = 0
nstvout = 250
nstfout = 0
nstenergy = 250
nstxtcout = 250
init_t = 0
delta_t = 0.002
xtcprec = 1000
nkx = 42
nky = 42
nkz = 84
pme_order = 4
ewald_rtol = 1e-05
ewald_geometry = 0
epsilon_surface = 0
optimize_fft = FALSE
ePBC = xyz
bUncStart = TRUE
bShakeSOR = FALSE
etc = Berendsen
epc = Berendsen
epctype = Isotropic
tau_p = 20
ref_p (3x3):
ref_p[ 0]={ 1.00000e+00, 0.00000e+00, 0.00000e+00}
ref_p[ 1]={ 0.00000e+00, 1.00000e+00, 0.00000e+00}
ref_p[ 2]={ 0.00000e+00, 0.00000e+00, 1.00000e+00}
compress (3x3):
compress[ 0]={ 4.50000e-05, 0.00000e+00, 0.00000e+00}
compress[ 1]={ 0.00000e+00, 4.50000e-05, 0.00000e+00}
compress[ 2]={ 0.00000e+00, 0.00000e+00, 4.50000e-05}
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 = 0.5
free_energy = no
init_lambda = 0
sc_alpha = 0
sc_power = 1
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: 51456
ref_t: 300
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
CPU= 0, lastcg= 8223, targetcg= 4112, myshift= 0
nsb->shift = 1, nsb->bshift= 0
Neighbor Search Blocks
nsb->nodeid: 0
nsb->nnodes: 1
nsb->cgtotal: 8224
nsb->natoms: 24594
nsb->shift: 1
nsb->bshift: 0
Nodeid index homenr cgload workload
0 0 24594 8224 8224
Max number of graph edges per atom is 4
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
Enabling SPC water optimization for 7441 molecules.
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 --- -------- --------
Center of mass motion removal mode is Linear
We have the following groups for center of mass motion removal:
0: rest, initial mass: 150847
There are: 24594 Atoms
Removing pbc first time
Done rmpbc
Started mdrun on node 0 Tue Mar 14 05:52:54 2006
Initial temperature: 430.169 K
Step Time Lambda
0 0.00000 0.00000
Grid: 10 x 10 x 20 cells
Configuring nonbonded kernels...
Testing AMD 3DNow support... not present.
Testing ia32 SSE support... present.
There are 24594 atoms in your xtc output selection
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