[gmx-users] membrane protein energy minimization error

[zhang]

 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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