Nilesh Dhumal wrote:
Hello,
I am trying to equilibrate my system, ionic liquids. My simulations gets
stop immediately. I reduced the step size. I modified initial structure.
I changed the box size. I checked force field parameters. I am using
opls foce field. I repeated my energy minimization 2-3 times. I could not
solve the problem. Every time i am geting following error message.
step 0Warning: 1-4 interaction between 20 and 27 at distance 3.803 which
is larger than the 1-4 table size 2.400 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size
Segmentation fault
Can you tell me how to solve this problem.
Please consult the following:
http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System
The prime suspect in my mind is your topology. How have you validated the
parameters for your ionic liquids? Does in vacuo minimization and short MD of
each component separately run stably? While OPLS is quite versatile,
parameterizing ionic liquids properly is not a trivial task, and is probably not
very straightforward.
-Justin
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 = 1.0
coulombtype = PME
vdwtype = cut-off
rcoulomb = 1.0
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 = v-rescale
tau_t = 0.1
tc-grps =system
ref_t = 300
; 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 = 300.0
gen_seed = 173529
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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