[gmx-users] Simulation problem

[Jernej Zidar]

Hi.
  I've been running some polymer simulations on our cluster and I'm
getting this error:
One of the box vectors has become shorter than twice the cut-off
length or box_yy-|box_zy| or box_zz has become smaller than the
cut-off.

  What does this error mean? I imagine it is somehow related to the
unit cell. Could the error be related to the fact that the unit cell
is rather long (along x axis) but short along the other axis. The
thickness of the solvation layer is 2.0 nm, which should be OK.

  I use the following input:
; Run parameters
integrator      = md            ; leap-frog integrator
nsteps          = 25000000      ; 2 * 25000000 = 50 ns
dt              = 0.002         ; 2 fs

; Bond parameters
continuation            =       yes     ; Restarting after NVT
constraint_algorithm    =       lincs   ; holonomic constraints
constraints             =       hbonds  ; all bonds (even heavy atom-H
bonds) constrained
lincs_iter              =       1       ; accuracy of LINCS
lincs_order             =       4       ; also related to accuracy

; Output control
nstxout         = 10000         ; save coordinates every 20 ps
nstenergy       = 1000          ; save energies every 20 ps
nstlog          = 1000          ; update log file every 20 ps

; Neighbour searching
ns_type         = grid
nstlist         = 5
rlist           = 1.2           ; short-range neighborlist cutoff (in nm)

; Non-bonded interactions
vdw-type        = shift
rvdw            = 1.0           ; short-range van der Waals cutoff (in nm)
rvdw-switch     = 0.8

; Electrostatics
coulombtype     = PME           ; Particle Mesh Ewald for long-range
electrostatics
rcoulomb        = 1.2           ; short-range electrostatic cutoff (in nm)
pme_order       = 4             ; cubic interpolation
fourierspacing  = 0.12          ; grid spacing for FFT
optimize-fft    = yes           ; optimize the FFT transforms for the
current problem

; Temperature coupling is on for three groups
tcoupl          = Nose-Hoover           ; More accurate thermostat
tc-grps         = POLYMER Water_CL_NA   ; three coupling groups - more accurate
tau_t           = 0.5   0.5             ; time constant, in ps
ref_t           = 300   300             ; reference temperature, one
for each group, in K

; Pressure coupling is on
pcoupl          = Parrinello-Rahman     ; Pressure coupling on in NPT
pcoupltype      = isotropic             ; uniform scaling of x-y box
vectors, independent z
tau_p           = 5.0                   ; time constant, in ps
ref_p           = 1.0                   ; reference pressure, x-y, z (in bar)
compressibility = 4.5e-5                ; isothermal compressibility, bar^-1

; Miscelanous
gen_vel         = no    ; Velocity generation is off
dispcorr        = no    ; account for cut-off vdW scheme

; Center of mass (COM) motion removal
; Reason: these options remove motion of the protein/bilayer relative
to the solvent/ions
nstcomm         = 10
comm-mode       = Linear
comm-grps       = POLYMER Water_CL_NA

- - -

Thanks in advance for any help or advice,
Jernej Zidar