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

[Justin A. Lemkul]

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

========================================