Nilesh Dhumal wrote:
Hello,
I am trying to equilibrate a ionic liquid system (EMI-BF4) in Gromacs
4.0.5 version. I am getting the following error during the minimization.
Is there any problem in input file.
I got following error:
Nilesh
Fatal error: The box size in direction X (1.799866) times the triclinic
skew factor (1.000000) is too small for a cut-off of 0.900000 with 2
domain decomposition cells, use 1 or more than 2 processors or increase
the box size in this direction
I think this error arises since domain decomposition is failing (which you can
read more about in the manual), but the underlying cause is really that your box
size no longer satisfies the minimum image convention: 0.9 * 2 > 1.799866.
-Justin
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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