[gmx-users] Unexplained crashes with Gromacs-4.0

[Justin A. Lemkul]

Hi,

I've gotten the following error with two of my simulation systems.  Usually this 
weird "variable ci" error means the system is unstable, and I've seen it before 
when I've done a poor job of equilibrating.  But now I'm seeing it a long time 
into my simulations (after 48 ns in one case, 60 ns in the other).  If I simply 
re-submit the job, it runs fine.  The error shown is as follows:

-------------------------------------------------------
Program mdrun_4.0_mpi, VERSION 4.0
Source code file: nsgrid.c, line: 357

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 180. It should have been within [ 0 .. 180 ]

-------------------------------------------------------

It seems to me that this "ci" variable is still within the range of 0->180, if 
those values are inclusive.

My .mdp file is as follows:

title		= NPT simulation for a membrane protein
; Run parameters
integrator	= md
dt		= 0.002
nsteps		= 5000000	; 10000 ps (10 ns)
tinit		= 40000
nstcomm		= 1
; Output parameters
nstxout		= 50000		; every 100 ps
nstvout		= 50000
nstfout		= 50000
nstlog		= 5000		; every 10 ps
nstenergy	= 5000
nstxtcout	= 5000
; Bond parameters
constraint_algorithm 	= lincs
constraints		= all-bonds
continuation 		= yes
; Cut-off's and neighborsearching
nstlist		= 5
ns_type		= grid
rlist		= 1.2
rcoulomb	= 1.2
rvdw		= 1.2
; PME electrostatics parameters
coulombtype	= PME
fourierspacing  = 0.18
;fourier_nx	= 0
;fourier_ny 	= 0
;fourier_nz	= 0
pme_order	= 4
ewald_rtol	= 1e-5
optimize_fft	= yes
; Berendsen temperature coupling is on in three groups
Tcoupl	 	= Nose-Hoover
tc_grps		= Protein POPC SOL_NA+_CL-
tau_t		= 0.1 0.1 0.1
ref_t		= 310 310 310
; Pressure coupling is not on
Pcoupl		= Parrinello-Rahman
pcoupltype	= semiisotropic
tau_p		= 2.0		
compressibility	= 4.5e-5 4.5e-5
ref_p		= 1.0 1.0
; Generate velocities is off
gen_vel		= no
gen_temp	= 310
gen_seed	= 7041776
; Periodic boundary conditions are on in all directions
pbc		= xyz
; Long-range dispersion correction
DispCorr	= EnerPres

Any ideas what's going on?

Thanks,
Justin

-- 
========================================

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

========================================