On 2/25/13 1:01 AM, Jernej Zidar wrote:
Hi.
I've been running some polymer simulations on our cluster and I'm
getting this error:
One of the box vectors has become shorter than twice the cut-off
length or box_yy-|box_zy| or box_zz has become smaller than the
cut-off.
What does this error mean? I imagine it is somehow related to the
unit cell. Could the error be related to the fact that the unit cell
is rather long (along x axis) but short along the other axis. The
thickness of the solvation layer is 2.0 nm, which should be OK.
The error means that fluctuation of the unit cell dimensions will cause
violation of the minimum image convention. Either the simulation box has become
unstable and is going to crash, or you have larger fluctuations than you
anticipated in the pressure (and thus box size) when building the system.
-Justin
I use the following input:
; Run parameters
integrator = md ; leap-frog integrator
nsteps = 25000000 ; 2 * 25000000 = 50 ns
dt = 0.002 ; 2 fs
; Bond parameters
continuation = yes ; Restarting after NVT
constraint_algorithm = lincs ; holonomic constraints
constraints = hbonds ; all bonds (even heavy atom-H
bonds) constrained
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Output control
nstxout = 10000 ; save coordinates every 20 ps
nstenergy = 1000 ; save energies every 20 ps
nstlog = 1000 ; update log file every 20 ps
; Neighbour searching
ns_type = grid
nstlist = 5
rlist = 1.2 ; short-range neighborlist cutoff (in nm)
; Non-bonded interactions
vdw-type = shift
rvdw = 1.0 ; short-range van der Waals cutoff (in nm)
rvdw-switch = 0.8
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range
electrostatics
rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm)
pme_order = 4 ; cubic interpolation
fourierspacing = 0.12 ; grid spacing for FFT
optimize-fft = yes ; optimize the FFT transforms for the
current problem
; Temperature coupling is on for three groups
tcoupl = Nose-Hoover ; More accurate thermostat
tc-grps = POLYMER Water_CL_NA ; three coupling groups - more accurate
tau_t = 0.5 0.5 ; time constant, in ps
ref_t = 300 300 ; reference temperature, one
for each group, in K
; Pressure coupling is on
pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT
pcoupltype = isotropic ; uniform scaling of x-y box
vectors, independent z
tau_p = 5.0 ; time constant, in ps
ref_p = 1.0 ; reference pressure, x-y, z (in bar)
compressibility = 4.5e-5 ; isothermal compressibility, bar^-1
; Miscelanous
gen_vel = no ; Velocity generation is off
dispcorr = no ; account for cut-off vdW scheme
; Center of mass (COM) motion removal
; Reason: these options remove motion of the protein/bilayer relative
to the solvent/ions
nstcomm = 10
comm-mode = Linear
comm-grps = POLYMER Water_CL_NA
- - -
Thanks in advance for any help or advice,
Jernej Zidar
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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