[gmx-users] problem regarding range checking error

[kinshuk at chem.iitb.ac.in]

  Thanks for provoiding insight.
  I have gone through instructions for grompp for EM.I have gone through
manual.I breakup the structure in manageable chunks i.e. i seperately
run the EM & PR for SCN, GUD, Protein individally,every individual run
was successful nothing get breakdown.As pr your's instruction i loocked
every warning and i solved all. Now no warning is there but still i am
getting same error while running EM for whole system.what should be next
steps to resolve this problem of nonsense physics.
I will be thankful for you.
The em.mdp file is like this.
;
;	Input file
;
title                =  Octamer		; a string
cpp                  =  /lib/cpp		; c-preprocessor
dt                   =  0.002			; time step
integrator           =  steep
nsteps               =  4000			; number of steps
nstcomm              =  1			; reset c.o.m. motion
nstxout              =  2000			; write coords
nstvout              =  50			; write velocities
nstlog		   =  50			; print to logfile
nstenergy            =  50			; print energies
energygrps           =  protein
nstlist              =  10			; update pairlist
ns_type              =  grid
constraint_algorithm =  shake
shake_tol            = 0.0001
coulombtype          =  PME
vdwtype              =  shift
rlist                =  1.5			; cut-off for ns
rvdw                 =  1.4
rvdw_switch	         =  0.8
rcoulomb             =  1.5
rcoulomb_switch	   =  0.8
Tcoupl               =  yes			; temperature bath (yes,no)
ref_t		         =  298
tc_grps              =  Protein
tau_t		         =  0.1
gen_vel              =  yes			; generate initial velocities
gen_temp             =  298			; initial temperature
gen_seed             =  173529		; random seed
emtol                =  100
emstep               =  0.01



> kinshuk at chem.iitb.ac.in wrote:
>>  Thanks for giving me insight to resolve the problem regarding grompp.
>> Now i came across new problem regarding energy minimization
>
> Please start a new email thread for a new problem. The subject line is
> your best chance to attract someone who can help you, so make it
> succint, relevant and informative.
>
>> MDRUN(mdrun)step while giving this command to command prompt.
>> {mdrun -v -s em.tpr -o em.trr -e em.edr -c after_em.gro -g emlog.log }
>> I came across this problem which i am mentioning below.
>>
>>
>> Reading file em.tpr, VERSION 3.3.1 (single precision)
>> Loaded with Money
>>
>>
>> Back Off! I just backed up em.edr to ./#em.edr.2#
>> Steepest Descents:
>>    Tolerance (Fmax)   =  1.00000e+02
>>    Number of steps    =         4000
>> -------------------------------------------------------1.31850e+12,
>> atom=
>> 1924
>> Program mdrun, 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 -2147483648. It should have been within [ 0 .. 216
>>
>> Please report this to the mailing list (gmx-users at gromacs.org)
>> -------------------------------------------------------
>>
>> What should be problem? I am attaching  emergy minimization em.mdp file.
>
> This is symptomatic of the kinds of problems discussed here...
> http://wiki.gromacs.org/index.php/blowing_up
>
> Because grompp returned you a .tpr file, your topology may have been
> well-formed. You should run grompp again and pay particular attention to
> any warnings it gives you. Even if it doesn't warn you about anything,
> the odds are excellent that despite being well-formed grammatically, the
> contents of your .top file lead to nonsense physics. Then large force on
> atoms can cause the above symptoms in EM.
>
> You should check your topology carefully, consulting with Chapter 5 of
> the manual where you need to. Break the structure & topology up into
> manageable chunks, and try an EM on an isolated molecule of each type to
>   see which bit of the topology is broken.

> Mark
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