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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