[gmx-users] ask for help

[Jochen Hub]

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). 

Probably, you have colliging atoms. If two atoms have a distance of less
than approx 0.1nm you sometimes run into this error (check with
g_mindist). You can also try to switch from steep to cg (or vice versa)
as integrator.

Jochen

> 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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-- 
************************************************
Dr. Jochen Hub
Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
D-37077 Goettingen, Germany
Email: jhub[at]gwdg.de
Tel.: +49 (0)551 201-2312
************************************************