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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