[gmx-users] System Crashes

[Sheikh Imamul Hossain]

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