[gmx-users] equilibration + Segmentation fault

[Justin A. Lemkul]

Nilesh Dhumal wrote:
> Hello,
> 
> I am trying to equilibrate my system, ionic liquids. My simulations gets
> stop immediately. I reduced the step size. I modified  initial structure.
> I  changed the box size. I checked  force field parameters. I am using
> opls foce field. I repeated my energy minimization 2-3 times. I could not
> solve the problem. Every time i am geting following error message.
> 
> step 0Warning: 1-4 interaction between 20 and 27 at distance 3.803 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
> Segmentation fault
> 
> 
> 
> Can you tell me how to solve this problem.

Please consult the following:

http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System

The prime suspect in my mind is your topology.  How have you validated the 
parameters for your ionic liquids?  Does in vacuo minimization and short MD of 
each component separately run stably?  While OPLS is quite versatile, 
parameterizing ionic liquids properly is not a trivial task, and is probably not 
very straightforward.

-Justin

> Here I have pasted the eqilibration file.
> Nilesh
> 
> title               =  cpeptid position restraining
> cpp                 =  /usr/bin/cpp
> constraints         =  none
> integrator          =  md
> dt                  =  0.001    ; ps !
> nsteps              =  100000      ; total 1.0 ps.
> nstcomm             =  1
> nstxout             =  10000
> nstvout             =  10000
> 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 = v-rescale
> tau_t = 0.1
> tc-grps  =system
> ref_t =   300
> ; Pressure coupling is  on
> Pcoupl              = parrinello-rahman
> 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            =  300.0
> gen_seed            =  173529
> 
> 
> 
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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