[gmx-users] System Crashes
Sheikh Imamul Hossain
s.imamul.ku at gmail.com
Wed May 24 04:54:54 CEST 2017
Hi Gromacs User,
I am running a big system consisting of more than 5000 CG lipids molecules
in each monolayer and these monolayers are separated by 133000 CG water
molecules in a box 50*50*100. Everything run well up to equilibration (5
equilibration for 10ns ) but after 3 microsecond production run the box
dimension reduces to 49.37048* 49.37048*11.52813. I am looking for the
reason why z dimension reduced? I am not sure is it fine or not. For your
consideration here is my mdp file that used for production run
; VARIOUS PREPROCESSING OPTIONS =
title = Martini
cpp = /usr/bin/cpp
; RUN CONTROL PARAMETERS =
integrator = md
; start time and timestep in ps =
dt = 0.03
nsteps = 100000000
; number of steps for center of mass motion removal =
nstcomm = 100
comm-grps = DPPC_POPC W
; OUTPUT CONTROL OPTIONS =
; Output frequency for coords (x), velocities (v) and forces (f) =
nstxout = 5000
nstvout = 5000
nstfout = 5000
; Output frequency for energies to log file and energy file =
nstlog = 5000
nstenergy = 100
nstcalcenergy = 100
; Output frequency and precision for xtc file =
nstxtcout = 1000
xtc_precision = 100
; This selects the subset of atoms for the xtc file. You can =
; select multiple groups. By default all atoms will be written. =
xtc-grps =
; Selection of energy groups =
energygrps = DPPC_POPC W
; NEIGHBORSEARCHING PARAMETERS =
cutoff-scheme = Verlet
; nblist update frequency =
nstlist = 10
; ns algorithm (simple or grid) =
ns_type = grid
; Periodic boundary conditions: xyz or none =
pbc = xyz
verlet-buffer-tolerance = 0.005
rlist = 1.2
; OPTIONS FOR ELECTROSTATICS AND VDW =
; Method for doing electrostatics =
coulombtype = cutoff
coulomb-modifier = Potential-shift
rcoulomb = 1.2
rcoulomb-switch = 0
; Dielectric constant (DC) for cut-off or DC of reaction field =
epsilon_r = 15
; Method for doing Van der Waals =
vdw_type = cutoff
vdw-modifier = Potential-shift
rvdw = 1.2
rvdw-switch = 0.9
epsilon_rf = 0
; OPTIONS FOR WEAK COUPLING ALGORITHMS =
; Temperature coupling =
tcoupl = berendsen
nsttcouple = 2
; Groups to couple separately =
tc-grps = DPPC_POPC W
; Time constant (ps) and reference temperature (K) =
tau_t = 1.0 1.0
ref_t = 310 310
; Pressure coupling =
Pcoupl = berendsen
Pcoupltype = semiisotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar) =
tau_p = 12.0
compressibility = 5e-5 5e-5
ref_p = 1.0 1.0
; GENERATE VELOCITIES FOR STARTUP RUN =
gen_vel = yes
gen_temp = 310
gen_seed = 473529
; OPTIONS FOR BONDS =
constraints = none
; Type of constraint algorithm =
constraint_algorithm = Lincs
; Do not constrain the start configuration =
unconstrained_start = no
; Highest order in the expansion of the constraint coupling matrix =
lincs_order = 4
; Lincs will write a warning to the stderr if in one step a bond =
; rotates over more degrees than =
lincs_warnangle = 30
........................................
.......................................
If I change only the
Temperature coupling berendsen to V-rescale and the pressure coupling to as
; Pressure coupling =
Pcoupl = berendsen
Pcoupltype = surface-tension
; Time constant (ps), compressibility (1/bar) and reference P (bar) =
tau_p = 12.0
compressibility = 5e-5 0
ref_p = 400 1.0 ; (surface tension at 20mN/m)
without changing the other parameters then the system crashes in it's
first equilibration with a massage
Atom 187258 moved more than the distance allowed by the domain
decomposition (1.202000) in direction X
distance out of cell 1.499496
New coordinates: 15.700 32.272 14.594
Old cell boundaries in direction X: 0.000 14.432
New cell boundaries in direction X: 0.000 14.200
How can I solve this problem?
N.B. Sorry for the lengthy message .
Sincerely Your’s
Sheikh Imamul Hossain
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