[gmx-users] Range checking error

[SeungPyo Hong]

Dear gmx-users,

I run MD for a protein molecule solvated with water molecules.
Until now it works well, however strangely they started to crash, I don't
know the reason.
So, if anyone have similar problem please let me know the solution.
It seems like that NPT system might cause some problems.

Also, when I continue MD further, it works.
(Sometimes simulation crashes after 1 ns, but sometimes it crashes only
after 100 ps.)
Then, can I use those results for further studies?

This is the mdp file:
integrator  = md
nsteps      = 1500000
dt      = 0.002
nstlist     = 10
rlist       = 1.0
coulombtype = pme
rcoulomb    = 1.0
vdw-type    = cut-off
rvdw        = 1.0
tcoupl      = Berendsen
tc-grps     = protein non-protein
tau-t       = 0.1 0.1
ref-t       = 310 310
pcoupl      = Berendsen
pcoupltype  = isotropic
tau-p       = 1
ref-p       = 1.0
compressibility = 4.5e-5
constraints = all-bonds
constraint_algorithm = lincs
nstxout     = 1000
nstvout     = 10000
nstxtcout   = 100
nstenergy   = 100
; Generate velocity is on at 300 K
gen_vel     = yes
gen_temp    = 300.0
gen_seed    = 173529

This is the error message:
-------------------------------------------------------
Program mdrun_mpi_d, VERSION 3.3.1
Source code file: nsgrid.c, line: 226

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 3185. It should have been within [ 0 .. 3072 ]
Please report this to the mailing list (gmx-users at gromacs.org)
-------------------------------------------------------

"Interfacing Space and Beyond..." (P. J. Harvey)

Error on node 1, will try to stop all the nodes
Halting parallel program mdrun_mpi_d on CPU 1 out of 16

gcq#307: "Interfacing Space and Beyond..." (P. J. Harvey)

[1] MPI Abort by user Aborting program !
[1] Aborting program!
-------------------------------------------------------
-- 
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'God used beautiful mathematics in creating the world.'
-Paul Dirac
'But he created too many objects.'
-Seungpyo Hong

Seungpyo Hong
Master student at PBIL(Protein BioInformatics Lab.) in KAIST, Daejeon Korea
Tel. (82)-18-372-2468
sphong_ at kaist.ac.kr
sp1020 at gmail.com
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