[gmx-users] membrane protein energy minimization error

[Justin A. Lemkul]

Your system is exploding, i.e. you have severe atomic overlap somewhere.  Having 
no idea what you've done to construct your system, it is hard to give any useful 
advice.  It is probably best if you search the list archive for "variable ci" 
(it will return many useful posts) or search the wiki site for "blowing up."

-Justin

zhang wrote:
> 
>  
>  
>  Dear all
>     Thank you for browsing my question.When I run a K ion channel, I 
> added DOPC bilayer membrane, at the first mdrun, Gromacs 
> program got Range checking error:
> Explanation: During neighborsearching, we assign each particle to a grid
> based on its coordinates. If your system contains collisions or parameter
> errors that give particles very high velocities you might end up with some
> coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
> put these on a grid, so this is usually where we detect those errors.
> Make sure your system is properly energy-minimized and that the potential
> energy seems reasonable before trying again.
> Variable ci has value -2147483648. It should have been within [ 0 .. 24389 ]
>     Why this error appears?
> My em.mdp
>  
>  title = comp_dop_water
> cpp = /lib/cpp; locationof cpp on SGI
> define                = -DFLEX_SPC
> freezegrps            = protein
> freezedim             = y y y
> constraints           = none
> integrator            = steep
> dt                    = 0.002
> nsteps                = 3000
> nstlist               = 10
> ns_type               = grid
> rlist                 = 0.9
> coulombtype           = PME
> rcoulomb              = 0.9
> rvdw                  = 1.0
> fourierspacing        = 0.12
> fourier_nx            = 0
> fourier_ny            = 0
> fourier_nz            = 0
> pme_order             = 4
> ewald_rtol            = 1e-5
> optimize_fft          = yes
> ;
> ;        energy minimizing stuff
> ;
> emtol                 = 1000.0
> emstep                = 0.01
>  
>  
> Thank you!
> 
>  
> 
> 
> 
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-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
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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