[gmx-users] Re: Membrane Runs Crashing

[Neha]

Here's the full mdp file. Please let me know if you need anymore information
and thank you so much for helping!

; RUN CONTROL PARAMETERS =
integrator               = md
; start time and timestep in ps =
tinit                    = 0.0
dt                       = 0.02
nsteps                   = 50000000
; number of steps for center of mass motion removal =
nstcomm                  = 1
comm-grps                = DPPC W

; OUTPUT CONTROL OPTIONS =
; Output frequency for coords (x), velocities (v) and forces (f) =
nstxout                  = 50000
nstvout                  = 50000
nstfout                  = 0
; Output frequency for energies to log file and energy file =
nstlog                   = 10000
nstenergy                = 500
; Output frequency and precision for xtc file =
nstxtcout                = 10000
xtc_precision            = 1000
; 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 W

; NEIGHBORSEARCHING PARAMETERS =
; nblist update frequency =
nstlist                  = 10
; ns algorithm (simple or grid) =
ns_type                  = grid
; Periodic boundary conditions: xyz or none =
pbc                      = xyz
; nblist cut-off         =
rlist                    = 1.2

; OPTIONS FOR ELECTROSTATICS AND VDW =
; Method for doing electrostatics =
coulombtype              = Shift
rcoulomb_switch          = 0.0
rcoulomb                 = 1.2
; Dielectric constant (DC) for cut-off or DC of reaction field =
epsilon_r                = 15
; Method for doing Van der Waals =
vdw_type                 = Shift
; cut-off lengths        =
rvdw_switch              = 0.9
rvdw                     = 1.2
; Apply long range dispersion corrections for Energy and Pressure =
DispCorr                 = No

; OPTIONS FOR WEAK COUPLING ALGORITHMS =
; Temperature coupling   =
tcoupl                   = Berendsen
; Groups to couple separately =
tc-grps                  = DPPC W
; Time constant (ps) and reference temperature (K) =
tau_t                    = 1.0 1.0
ref_t                    = 325 325
; Pressure coupling      =
Pcoupl                   = berendsen
Pcoupltype               = semiisotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar) =
tau_p                    = 1.0  1.0
compressibility          = 5e-6 0.0
ref_p                    = 0.0  0.0

; GENERATE VELOCITIES FOR STARTUP RUN =
gen_vel                  = yes
gen_temp                 = 325
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



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