[gmx-users] Fatal error:

Nilesh Dhumal ndhumal at andrew.cmu.edu
Wed Jul 7 18:12:41 CEST 2010


Hello,

I am trying to equilibrate my system, ionic liquids. Simulations stops
with following error

Fatal error:
1 of the 43778 bonded interactions could not be calculated because some
atoms involved moved further apart than the multi-body cut-off distance
(1.32754 nm) or the two-body cut-off distance (1.6 nm), see option -rdd,
for pairs and tabulated bonds also see option -ddcheck.

Can you tell me how to solve this problem.
Here I have pasted the eqilibration file.
Nilesh

title               =  cpeptid position restraining
cpp                 =  /usr/bin/cpp
constraints         =  none
integrator          =  md
dt                  =  0.001    ; ps !
nsteps              =  100000      ; total 1.0 ps.
nstcomm             =  1
nstxout             =  10000
nstvout             =  10000
nstfout             =  0
nstlog              =  10
nstenergy           =  10
nstlist             =  10
ns_type             =  grid
rlist               =  1.2
coulombtype         = PME
vdwtype             = cut-off
rcoulomb            =  1.2
rvdw                =  1.6
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 = v-rescale
tau_t = 0.1
tc-grps  =system
ref_t =   600
; Pressure coupling is  on
Pcoupl              = parrinello-rahman
pcoupltype          = isotropic
tau_p               =  0.5
compressibility     =  4.5e-5
ref_p               =  1.0
; Generate velocites is on at 300 K.
gen_vel             =  yes
gen_temp            =  600.0
gen_seed            =  173529








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