[gmx-users] equilibration + Segmentation fault

[Justin A. Lemkul]

Nilesh Dhumal wrote:
> 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?

If it's something you've changed, and all the other components are working, then 
yes, I would suspect that there's likely a problem with whatever you've changed. 
  Please do consult the link I posted - it contains a "greatest hits" of sorts 
of the most useful advice I can come up with for diagnosing unstable systems.

-Justin

> 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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>>
> 
> 
> 

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

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

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