[gmx-users] Fatal error: The box size in direction X (1.799866) times the triclinic skew factor (1.000000) is too small for a cut-off of 0.900000 with 2 domain decomposition cells, use 1 or more than 2 processors or increase the box size in this direction

[Justin A. Lemkul]

Nilesh Dhumal wrote:
> Hello,
> 
> I am trying to equilibrate a ionic liquid system (EMI-BF4) in Gromacs
> 4.0.5 version.  I am getting the following error during the  minimization.
> Is there any problem in input file.
> 
> I got following error:
> 
> Nilesh
> Fatal error: The box size in direction X (1.799866) times the triclinic
> skew factor (1.000000) is too small for a cut-off of 0.900000 with 2
> domain decomposition cells, use 1 or more than 2 processors or increase
> the box size in this direction
> 

I think this error arises since domain decomposition is failing (which you can 
read more about in the manual), but the underlying cause is really that your box 
size no longer satisfies the minimum image convention: 0.9 * 2 > 1.799866.

-Justin

> 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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