[gmx-users] Erro in SMD simulation..

[Kalyanashis]

Dear all, 
    I am trying to run an SMD simulation of an enzyme system with a drug
molecule. The final SMD run was crashed at the middle of the MD run(crashed
at 1370 ps). I got an error and the erro is 
" Fatal error:
Distance of pull group 1 (8.662854 nm) is larger than 0.49 times the box
size (8.832091)"
I have checked for the solution in the gromacs user
forum(http://gromacs.5086.x6.nabble.com/Distance-of-pull-group-1-2-142226-nm-is-larger-than-0-49-times-the-box-size-2-184750-td5007938.html#a5007939,
http://gromacs.5086.x6.nabble.com/Pull-code-with-pull-geometry-cylinder-generates-error-Distance-of-pull-group-1-4-030185-nm-is-larger-td5001603.html#a5001695)
but I did get any information.
I have attache my smd.mdp file
title                  =  2JEY-HI6
cpp                    =  /usr/bin/cpp
constraints            =  all-bonds
integrator             =  md
dt                     =  0.001 ; ps !
nsteps                 =  5000000 ; total 2 ns.
nstcomm                =  100
nstxout                =  500; collect data every 1 ps
;nstxtcout              =  500
;xtc_precision          =  1000
nstvout                =  1000
nstfout                =  0
nstenergy              =  100
nstlog                 =  100
nstlist                =  100
ns_type                =  grid
pbc                   =  xyz
rlist                  =  1.0
coulombtype            =  PME
rcoulomb               =  1.0
vdwtype                =  cutoff
rvdw                   =  1.4
fourierspacing         =  0.12
fourier_nx             =  0
fourier_ny             =  0
fourier_nz             =  0
pme_order              =  4
ewald_rtol             =  1e-5
optimize_fft           =  yes
; Berendsen temperature coupling is on
Tcoupl              =  berendsen
tau_t               =  0.5       
tcgrps              =  system    
ref_t               =  300       
; Pressure coupling is on
Pcoupl              =  berendsen
pcoupltype          =  isotropic ; Use semiisotropic when working with
membranes
tau_p               =  2.0
compressibility     =  4.5e-5
ref_p               =  1.0
refcoord-scaling    =  all
; Generate velocites is on at 300 K.
gen_vel             =  yes
gen_temp            =  300.0
gen_seed            =  173529
;COM pulling
pull                     = umbrella
pull_geometry            = distance
pull_dim                 = N N Y
pull_r1                  = 1
pull_r0                  = 1
;pull_constr_tot          = 1e-6
pull_start               = yes
pull_nstxout             = 10
pull_nstfout             = 1
pull_ngroups             = 1
;name of reference group
pull_group0              = Protein
;pull_weights             = 0
;name of pull group
pull_group1              = UNK
;pull_weights             = 0
pull_vec1                = 0.0 0.0 -1
;ref. distance at t=0
;pull_init1               = -2.4477384   -1.0229216   -1.5900776
;rate of change of ref. gr. [nm/ps]
pull_rate1               = 0.0005
;force constant [KJ mol^-1 nm^-2]
pull_k1                  = 1586.747
;pull_kB1                =

I changed the pull_k1, added pbc=xyz but nothing is working. One of friend
got same problem but pbc=xyz was working for his system. 
Please suggest me any probable solution.


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