[gmx-users] "Range checking error" issue

[Matteo Guglielmi]

David van der Spoel wrote:
> 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.
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>
>
I did what you suggest and even more, I decreased the timestep to 0.001

Well the problem doesn't go away.

I've been reading mails from this discussion list... I'm not the only
who's experiencing this kind of problem (ci variable range error)...
actually few gmx users suggest it comes only from parallel runs which
is my case BTW.

I'm running parallel runs on different clusters... it's happening
everywhere.