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

[Mark Abraham]

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.
> 
> Is the problem in mdp file?

No, there's something nonphysical about your starting structure, and 
it's blowing up. See 
http://www.gromacs.org/Documentation/Errors#1-4_interaction_not_within_cut-off 
Go and have a look at your structure to start with :-)

Mark

> 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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