[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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