[gmx-users] Fatal error:

[Justin A. Lemkul]

Nilesh Dhumal wrote:
> Hello,
> 
> I am trying to equilibrate my system, ionic liquids. Simulations stops
> with following error
> 
> Fatal error:
> 1 of the 43778 bonded interactions could not be calculated because some
> atoms involved moved further apart than the multi-body cut-off distance
> (1.32754 nm) or the two-body cut-off distance (1.6 nm), see option -rdd,
> for pairs and tabulated bonds also see option -ddcheck.
> 
> Can you tell me how to solve this problem.

Sounds like the system is blowing up.

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

-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               =  1.2
> coulombtype         = PME
> vdwtype             = cut-off
> rcoulomb            =  1.2
> rvdw                =  1.6
> 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 =   600
> ; 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            =  600.0
> 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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