[gmx-users] Simulation problem
Jernej Zidar
jernej.zidar at gmail.com
Mon Feb 25 07:01:08 CET 2013
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.
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
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