[gmx-users] equilibration + Segmentation fault

[Nilesh Dhumal]

I am using the opls parameters from Lope's paper.
In vaccum energy minimzatin is working well. MD is not at all working.

My other systems are running well. In the present system I changed the
anion, cation parameters are fine.
 Is the problem with anion parameters?
Nilesh

On Fri, June 4, 2010 10:20 pm, Justin A. Lemkul wrote:
>

>
> 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
>
>
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