[gmx-users] problems with nsgrid
Gianfranco Bocchinfuso
gianfranco.bocchinfuso at uniroma2.it
Tue Feb 27 11:46:43 CET 2007
Dear gmx users
I'm simulating a system with 128 POPC, 5000 water (SPC) and 1 peptide with
dummy hydrogens (option -vsite hydrogens in pdb2gmx) and 4fs of time step
to reproduce the bilayer assembling, starting from molecules randomly placed
inside the box. The system has been minimized and an equilibration MD of 100
ps has been successful carried out (isotropic pressure coupling and peptide
positions constrained). During the second run (with peptide unconstrained
and anisotropic pressure coupling) the simulation crashes at different time
(from 150 ps to 3200ps) depending from setting (i.e. shake/lincs, with and
without shuffle/sort options, but also (:o()) changing the frequency of
output ???).
Below I report the message that appears at the crash of simulations and also
the log file for node 3 and an example of mdp file used.
Thank you in advance
Gianfranco
Program mdrun_mpi_d, 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.
Error on node 3, will try to stop all the nodes
Halting parallel program mdrun_mpi_d on CPU 3 out of 4
This is the logfile for node 3
Log file opened on Mon Feb 26 17:54:59 2007
Host: node10 pid: 20538 nodeid: 3 nnodes: 4
The Gromacs distribution was built Wed Oct 4 13:03:06 CEST 2006 by
bocchinfuso at fermi2 (Linux 2.6.9-1.667smp i686)
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 4000 data points for Ewald.
Tabscale = 2000 points/nm
Generated table with 4000 data points for LJ6.
Tabscale = 2000 points/nm
Generated table with 4000 data points for LJ12.
Tabscale = 2000 points/nm
Generated table with 2000 data points for 1-4 COUL.
Tabscale = 2000 points/nm
Generated table with 2000 data points for 1-4 LJ6.
Tabscale = 2000 points/nm
Generated table with 2000 data points for 1-4 LJ12.
Tabscale = 2000 points/nm
Enabling SPC water optimization for 5000 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 --- -------- --------
Parallelized PME sum used.
PARALLEL FFT DATA:
local_nx: 15 local_x_start: 45
local_ny_after_transpose: 15 local_y_start_after_transpose 45
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: 188438
There are: 5435 Atoms
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 --- -------- --------
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
J. P. Ryckaert and G. Ciccotti and H. J. C. Berendsen
Numerical Integration of the Cartesian Equations of Motion of a System with
Constraints; Molecular Dynamics of n-Alkanes
J. Comp. Phys. 23 (1977) pp. 327-341
-------- -------- --- Thank You --- -------- --------
Going to use C-settle (1257 waters)
wo = 0.888096, wh =0.0559521, wohh = 18.0154, rc = 0.08165, ra = 0.00646074
rb = 0.0512738, rc2 = 0.1633, rone = 1, dHH = 0.1633, dOH = 0.1
Constraining the coordinates at t0-dt (step -1)
Started mdrun on node 3 Mon Feb 26 17:55:12 2007
Grid: 13 x 13 x 13 cells
Configuring nonbonded kernels...
Testing ia32 SSE2 support... present.
Grid: 14 x 13 x 13 cells
Grid: 13 x 13 x 13 cells
Grid: 14 x 13 x 13 cells
Grid: 13 x 13 x 13 cells
Grid: 14 x 13 x 13 cells
Grid: 13 x 13 x 13 cells
Grid: 14 x 13 x 13 cells
Grid: 13 x 13 x 13 cells
Grid: 14 x 13 x 13 cells
Grid: 13 x 13 x 13 cells
Grid: 14 x 13 x 13 cells
Grid: 13 x 13 x 13 cells
Grid: 14 x 13 x 13 cells
Grid: 13 x 13 x 13 cells
Grid: 14 x 13 x 13 cells
Grid: 13 x 13 x 13 cells
Grid: 14 x 13 x 13 cells
Grid: 13 x 13 x 13 cells
Grid: 14 x 13 x 13 cells
Grid: 13 x 13 x 13 cells
Grid: 14 x 13 x 13 cells
Grid: 13 x 13 x 13 cells
Grid: 14 x 13 x 13 cells
Grid: 13 x 13 x 13 cells
Grid: 14 x 13 x 13 cells
Grid: 13 x 13 x 13 cells
Grid: 14 x 13 x 13 cells
Grid: 13 x 13 x 13 cells
Grid: 14 x 13 x 13 cells
Grid: 13 x 13 x 13 cells
Grid: 14 x 13 x 13 cells
Grid: 13 x 13 x 13 cells
Grid: 14 x 13 x 13 cells
Grid: 13 x 13 x 13 cells
Grid: 14 x 13 x 13 cells
Grid: 13 x 13 x 13 cells
Grid: 14 x 13 x 13 cells
Grid: 13 x 13 x 13 cells
Grid: 14 x 13 x 13 cells
Grid: 14 x 13 x 12 cells
Grid: 14 x 13 x 13 cells
Grid: 14 x 13 x 12 cells
Grid: 14 x 13 x 13 cells
Grid: 14 x 13 x 12 cells
Grid: 14 x 13 x 13 cells
Grid: 14 x 13 x 12 cells
Grid: 14 x 13 x 13 cells
Grid: 14 x 13 x 12 cells
Grid: 14 x 13 x 13 cells
Grid: 14 x 13 x 12 cells
Grid: 15 x 13 x 12 cells
Grid: 14 x 13 x 12 cells
Grid: 15 x 13 x 12 cells
Grid: 14 x 13 x 12 cells
Grid: 15 x 13 x 12 cells
Grid: 14 x 13 x 12 cells
Grid: 15 x 13 x 12 cells
Grid: 14 x 13 x 12 cells
Grid: 15 x 13 x 12 cells
Grid: 14 x 13 x 12 cells
Grid: 15 x 13 x 12 cells
Grid: 14 x 13 x 12 cells
Grid: 15 x 13 x 12 cells
Grid: 14 x 13 x 12 cells
Grid: 15 x 13 x 12 cells
Grid: 14 x 13 x 12 cells
-------------------------------------------------------
Program mdrun_mpi_d, 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 2228. It should have been within [ 0 .. 2184 ]
Please report this to the mailing list (gmx-users at gromacs.org)
-------------------------------------------------------
"killing children ..." (Insight/Parasoft)
and finally this is (just an example) of mdp file used during simulations
; VARIOUS PREPROCESSING OPTIONS =
title = Yo
cpp = /lib/cpp
include = -I../top
define =
; RUN CONTROL PARAMETERS =
integrator = md
; start time and timestep in ps
tinit = 0
dt = 0.004
nsteps = 12500000; 100ps
; number of steps for center of mass motion removal =
comm_mode = Linear ;Remove center of mass translation
nstcomm = 1
comm-grps =
; LANGEVIN DYNAMICS OPTIONS =
; Temperature, friction coefficient (amu/ps) and random seed =
bd-temp = 300
bd-fric = 0
ld-seed = 1993
; ENERGY MINIMIZATION OPTIONS =
; Force tolerance and initial step-size =
emtol = 1000
emstep = 0.01
; Max number of iterations in relax_shells =
niter = 1000
; Frequency of steepest descents steps when doing CG =
nstcgsteep = 1000
; OUTPUT CONTROL OPTIONS =
; Output frequency for coords (x), velocities (v) and forces (f) =
nstxout = 2500 ;10ps
nstvout = 2500
nstfout = 0
; Output frequency for energies to log file and energy file =
nstlog = 100 ;0.4ps
nstenergy = 100
; Output frequency and precision for xtc file =
nstxtcout = 100 ;out every 0.4ps
xtc-precision = 1000
; This selects the subset of atoms for the xtc file. You can =
; select multiple groups. By default all atoms will be written. =
xtc_grps =
; Selection of energy groups =
energygrps = Protein POPC SOL
; NEIGHBORSEARCHING PARAMETERS =
; nblist update frequency =
nstlist = 10
; ns algorithm (simple or grid) =
ns_type = grid
; Periodic boundary conditions: xyz or none =
pbc = xyz
; nblist cut-off =
rlist = 1.0
domain-decomposition = no
; OPTIONS FOR ELECTROSTATICS AND VDW =
; Method for doing electrostatics =
coulombtype = PME
rcoulomb-switch = 0
rcoulomb = 1.0
; Dielectric constant (DC) for cut-off or DC of reaction field =
epsilon-r = 1
; Method for doing Van der Waals =
vdw-type = Cut-off
; cut-off lengths =
rvdw-switch = 0
rvdw = 1.0
; Apply long range dispersion corrections for Energy and Pressure =
DispCorr = No
; Spacing for the PME/PPPM FFT grid =
fourierspacing = 0.12
; FFT grid size, when a value is 0 fourierspacing will be used =
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
; EWALD/PME/PPPM parameters =
pme_order = 4
ewald_rtol = 1e-05
epsilon_surface = 0
optimize_fft = no
; OPTIONS FOR WEAK COUPLING ALGORITHMS =
; Temperature coupling =
tcoupl = Berendsen
; Groups to couple separately =
tc-grps = Protein POPC SOL
; Time constant (ps) and reference temperature (K) =
tau_t = 0.1 0.1 0.1
ref_t = 300 300 300
; Pressure coupling =
Pcoupl = Berendsen
Pcoupltype = anisotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar) =
tau_p = 1.0
compressibility = 4.5e-5 4.5e-5 4.5e-5 0.0 0.0 0.0
ref_p = 1.0 1.0 1.0 0.0 0.0 0.0
; SIMULATED ANNEALING CONTROL =
annealing = no no no
; Time at which temperature should be zero (ps) =
zero-temp_time = 0 0 0
; GENERATE VELOCITIES FOR STARTUP RUN =
gen_vel = no
gen_temp = 300
gen_seed = 173529
; OPTIONS FOR BONDS =
constraints = all-bonds
; Type of constraint algorithm =
constraint-algorithm = shake
; Do not constrain the start configuration =
unconstrained-start = no
; Relative tolerance of shake =
shake-tol = 0.0001
; Highest order in the expansion of the constraint coupling matrix =
lincs-order = 4
; Lincs will write a warning to the stderr if in one step a bond =
; rotates over more degrees than =
lincs-warnangle = 30
; Convert harmonic bonds to morse potentials =
morse = no
; NMR refinement stuff =
; Distance restraints type: No, Simple or Ensemble =
disre = No
; Force weighting of pairs in one distance restraint: Equal or Conservative
=
disre-weighting = Equal
; Use sqrt of the time averaged times the instantaneous violation =
disre-mixed = no
disre-fc = 1000
disre-tau = 0
; Output frequency for pair distances to energy file =
nstdisreout = 100
; Free energy control stuff =
free-energy = no
init-lambda = 0
delta-lambda = 0
sc-alpha = 0
sc-sigma = 0.3
; Non-equilibrium MD stuff =
acc-grps =
accelerate =
freezegrps =
freezedim =
cos-acceleration = 0
energygrp_excl =
; Electric fields =
; Format is number of terms (int) and for all terms an amplitude (real) =
; and a phase angle (real) =
E-x =
E-xt =
E-y =
E-yt =
E-z =
E-zt =
; User defined thingies =
user1-grps =
user2-grps =
userint1 = 0
userint2 = 0
userint3 = 0
userint4 = 0
userreal1 = 0
userreal2 = 0
userreal3 = 0
userreal4 = 0
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