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

[Yongchul Chung]

I think your box is too small. try changing them.

On Tue, Oct 13, 2009 at 8:05 PM, Justin A. Lemkul <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 | (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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