[gmx-users] p0_22967: p4_error: interrupt SIGSEGV: 11

[Justin A. Lemkul]

Nilesh Dhumal wrote:
> Hello,
> 
> I am trying to equilibrate a ionic liquid system (EMI-BF4) in Gromacs
> 4.0.5 version.  If I reduce the box size to get expt. density,  I get the
> error immidiately after the mdrun starts
> p0_22967:  p4_error: interrupt SIGSEGV: 11
> 
> If I increase the box size the simulation goes ok. But the density gets
> lower.
> Is the problem in mdp file?

If one system is immediately seg faulting, and the other system is giving the 
wrong results, the first thing I would suspect is that the parameters you're 
using for your ionic liquid are wrong.  A good model will give the right 
density, regardless of box size.

What have you done in terms of EM or equilibration?  How are you coming up with 
your parameters?

-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               =  0.9
> coulombtype         = PME
> vdwtype             = cut-off
> rcoulomb            =  0.9
> rvdw                =  0.9
> 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 =   600
> ; 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            =  600.0
> 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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