[gmx-users] Cutoff length

[fsaadedi at staffmail.ed.ac.uk]

Dear Users,

I'm running a simulation with a peptide in water but the simulation 
crashed after 600ns.
Fatal error: One of the box vectors has become shorter than twice the 
cut-off length.
I include my mdp file to see if there are noticeable errors.

Any ideas on what may be causing the problem would be much appreciated.

Thank you in advance for your time in this matter.

Farid Sa'adedin

; PREPROCESSING
title                  = Bac7alphawater
cpp                    = /lib/cpp
include                = -I.

; RUN CONTROL
integrator             = md
tinit                  = 0
dt                     = 0.002
nsteps                 = 1500000
nstcomm                = 10

; LANGEVIN DYNAMICS

; ENERGY MINIMIZATION
emtol                  = 1000.0
emstep                 = 0.01
nstcgsteep             = 1000

; SHELL MOLECULAR DYNAMICS

; OUTPUT CONTROL
nstxout                = 10000
nstvout                = 10000
nstfout                = 10000
nstlog                 = 10000
nstenergy              = 10000
nstxtcout              = 10000

; NEIGHBOR SEARCHING
nstlist                = 1.0
ns_type                = grid
pbc                    = xyz
rlist                  = 1.0

; ELECTROSTATICS AND VDW
coulombtype            = Reaction-Field
rcoulomb               = 1.8
epsilon_r              = 100.0
vdwtype                = Cut-off
rvdw                   = 1.0
dispcorr               = no

; TEMPERATURE COUPLING
tcoupl                 = berendsen
tau_t                  = 0.1
ref_t                  = 300
tc_grps                = System

; PRESSURE COUPLING
pcoupl                 = berendsen
pcoupltype             = isotropic
tau_p                  = 5.0 5.0 5.0
compressibility        = 4.5e-5 4.5e-5 4.5e-5
ref_p                  = 1.0 1.0 1.0

; SIMULATED ANNEALING
annealing              = no
zero_temp_time         = 100

; VELOCITY GENERATION
gen_vel                = no


;BONDS
constraints            = none
;constraint_algorithm   = shake
morse                  = no

; ENERGY GROUP EXCLUSIONS

; NMR REFINEMENT

; FREE ENERGY PERTUBATION
free_energy             = no

; NON-EQULIBRIUM MD

; ELECTRIC FIELDS