Nilesh Dhumal wrote:
Hello,
I am trying to equilibrate a ionic liquid system (EMI-BF4) in Gromacs
4.0.5 version. If I reduce the box size to get expt. density, I get the
error immidiately after the mdrun starts
p0_22967: p4_error: interrupt SIGSEGV: 11
If I increase the box size the simulation goes ok. But the density gets
lower.
Is the problem in mdp file?
If one system is immediately seg faulting, and the other system is giving the
wrong results, the first thing I would suspect is that the parameters you're
using for your ionic liquid are wrong. A good model will give the right
density, regardless of box size.
What have you done in terms of EM or equilibration? How are you coming up with
your parameters?
-Justin
Nilesh
Here is my pr.mdp file
title = cpeptid position restraining
cpp = /usr/bin/cpp
constraints = none
integrator = md
dt = 0.002 ; ps !
nsteps = 200000 ; total 1.0 ps.
nstcomm = 1
nstxout = 10
nstvout = 1000
nstfout = 0
nstlog = 10
nstenergy = 10
nstlist = 10
ns_type = grid
rlist = 0.9
coulombtype = PME
vdwtype = cut-off
rcoulomb = 0.9
rvdw = 0.9
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 = 0.1
tc-grps =system
ref_t = 600
; Pressure coupling is on
Pcoupl = Berendsen
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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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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