[gmx-users] "Range checking error" issue

[David van der Spoel]

Matteo Guglielmi wrote:
> Hello world,
> 
> the following is my input file:
> 
> ########
> title                    = 2masn
> cpp                      = /usr/bin/cpp
> define                   = -DPOSRES
> integrator               = md
> tinit                    = 0
> dt                       = 0.002
> nsteps                   = 1500000
> init_step                = 0
> comm_mode                = Angular
> nstcomm                  = 1
> comm_grps                = Pore
> nstxout                  = 250000
> nstvout                  = 250000
> nstfout                  = 250000
> nstcheckpoint            = 1000
> nstlog                   = 2500
> nstxtcout                = 2500
> xtc_grps                 = System
> energygrps               = Pore Membrane Ions Water
> nstenergy                = 2500
> nstlist                  = 5
> ns_type                  = grid
> pbc                      = xyz
> rlist                    = 1.0
> coulombtype              = PME
> rcoulomb                 = 1.0
> vdwtype                  = Cut-off
> rvdw                     = 1.4
> fourier_nx               = 88
> fourier_ny               = 88
> fourier_nz               = 88
> pme_order                = 4
> ewald_rtol               = 1e-5
> ewald_geometry           = 3d
> optimize_fft             = yes
> tcoupl                   = berendsen
> tc_grps                  = Solute Solvent
> tau_t                    = 0.1    0.4
> ref_t                    = 300    300
> pcoupl                   = berendsen
> pcoupltype               = anisotropic
> tau_p                    = 0.5      0.5      0.5      0.5    0.5    0.5
> compressibility          = 4.53e-5  4.53e-5  4.53e-5  0.0    0.0    0.0
> ref_p                    = 1.025    1.025    1.025    1.025  1.025  1.025
> gen_vel                  = yes
> gen_temp                 = 300
> gen_seed                 = 173529
> constraints              = all-bonds
> constraint_algorithm     = lincs
> unconstrained_start      = no
> lincs_order              = 4
> lincs_iter               = 2
> lincs_warnangle          = 30
> ################
> 
> and way after the very beginning of this simulation (~1.5ns) I always
> get this error message:
> 
> ##########
>    Rel. Constraint Deviation:  Max    between atoms     RMS
>        Before LINCS         0.032676  17797  17799   0.003970
>         After LINCS         0.000004  17162  17169   0.000000
> 
> Grid: 10 x 11 x 12 cells
> Grid: 10 x 12 x 12 cells
> Grid: 10 x 11 x 12 cells
> Grid: 10 x 12 x 12 cells
> Grid: 10 x 11 x 12 cells
> Grid: 10 x 12 x 12 cells
> Grid: 10 x 11 x 12 cells
> Grid: 10 x 12 x 12 cells
> Grid: 10 x 11 x 12 cells
> -------------------------------------------------------
> Program mdrun_mpi, 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 .. 1320 ]
> Please report this to the mailing list (gmx-users at gromacs.org)
> -------------------------------------------------------
> #################
> 
> Is my input file so bad?

I would increase tau_p to at least 5 ps for anisotropic coupling.

> 
> (I've seen people using lincs with 5fs time step...)
> 
> Thanks for any useful suggestion,
> MG.
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php


-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++