[gmx-users] problems with nsgrid
Gianfranco Bocchinfuso
gianfranco.bocchinfuso at uniroma2.it
Mon Mar 5 10:45:45 CET 2007
The previous e-mail refers to simulation running with mdrun in double
precision, using the single precision the problem is disappered.
Regards
Gianfranco
----- Original Message -----
From: "Gianfranco Bocchinfuso" <gianfranco.bocchinfuso at uniroma2.it>
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Sent: Tuesday, February 27, 2007 11:46 AM
Subject: [gmx-users] problems with nsgrid
> 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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