[gmx-users] p0_4238: p4_error: interrupt SIGSEGV: 11

[Yongchul Chung]

I jumped to the conclusion too fast. Thanks Justin for correcting me.
Disregard my previous comment please.

On Tue, Oct 13, 2009 at 10:35 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Yongchul Chung wrote:
>
>> I think your box is too small. try changing them.
>>
>>
> What leads you to this conclusion?  We have no information about the box.
> Presumably, the only box that is "too small" would be one that doesn't
> satisfy the minimum image convention, but grompp fails with a fatal error in
> that case.
>
> -Justin
>
>  On Tue, Oct 13, 2009 at 8:05 PM, Justin A. Lemkul <jalemkul at vt.edu<mailto:
>> jalemkul at vt.edu>> wrote:
>>
>>
>>
>>    Nilesh Dhumal wrote:
>>
>>        Hello,
>>
>>        I am trying to equilibrate glucose in water using Gromacs
>>        4.0.5 version.  I am geting the error immidiately after the
>>        mdrun starts
>>        Warning: 1-4 interaction between 1 and 18 at distance 3.462 which
>> is
>>        larger than the 1-4 table size 2.400 nm
>>        These are ignored for the rest of the simulation
>>        This usually means your system is exploding,
>>        if not, you should increase table-extension in your mdp file
>>        or with user tables increase the table size
>>        p0_4238:  p4_error: interrupt SIGSEGV: 11
>>        Killed by signal 2.
>>
>>
>>    Have you searched the website?  You would have undoubtedly found this:
>>
>>
>>
>> http://www.gromacs.org/Documentation/Errors#1-4_interaction_not_within_cut-off
>>
>>    You should also search the list archive.  This problem shows up
>>    weekly, if not daily sometimes.
>>
>>
>>        Is the problem in mdp file?
>>
>>
>>    Nothing seems obviously wrong.
>>
>>    -Justin
>>
>>
>>        Nilesh
>>
>>        Here is my pr.mdp file
>>        title               =  cpeptid position restraining
>>        cpp                 =  /usr/bin/cpp
>>        constraints         =  none
>>        integrator          =  md
>>        dt                  =  0.002    ; ps !
>>        nsteps              =  200000      ; total 1.0 ps.
>>        nstcomm             =  1
>>        nstxout             =  10
>>        nstvout             =  1000
>>        nstfout             =  0
>>        nstlog              =  10
>>        nstenergy           =  10
>>        nstlist             =  10
>>        ns_type             =  grid
>>        rlist               =  1.0
>>        coulombtype         = PME
>>        vdwtype             = cut-off
>>        rcoulomb            =  1.0
>>        rvdw                =  1.4
>>        fourierspacing      = 0.12
>>        fourier_nx               = 0
>>        fourier_ny               = 0
>>        fourier_nz               = 0
>>        pme_order           = 4
>>        ewald_rtol          = 1e-5
>>        optimize_fft        = yes
>>        ; Berendsen temperature coupling is on
>>        Tcoupl = Berendsen
>>        tau_t = 0.1
>>        tc-grps  =system
>>        ref_t =   350
>>        ; Pressure coupling is  on
>>        Pcoupl              = Berendsen
>>        pcoupltype          = isotropic
>>        tau_p               =  0.5
>>        compressibility     =  4.5e-5
>>        ref_p               =  1.0
>>        ; Generate velocites is on at 300 K.
>>        gen_vel             =  yes
>>        gen_temp            =  350.0
>>        gen_seed            =  173529
>>
>>
>>
>>
>>
>>
>>
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>>
>>    --    ========================================
>>
>>    Justin A. Lemkul
>>    Ph.D. Candidate
>>    ICTAS Doctoral Scholar
>>    Department of Biochemistry
>>    Virginia Tech
>>    Blacksburg, VA
>>    jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>>    http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>>    ========================================
>>
>>    _______________________________________________
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>>
>>
>>
>>
>> --
>> Yongchul "Greg" Chung
>> Graduate Student
>> Dept. of Chemical Engineering, Case Western Reserve University
>>
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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-- 
Yongchul "Greg" Chung
Graduate Student
Dept. of Chemical Engineering, Case Western Reserve University
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