; VARIOUS PREPROCESSING OPTIONS =
title = Yo
cpp = /usr/bin/cpp
include =
define =
; RUN CONTROL PARAMETERS =
integrator = md
;
; for polarizable water minimization do not forget to replace the
; constraints by stiff bonds (force constant of 50000)
;
; start time and timestep in ps =
tinit = 0.0
dt = 0.020
;
; Polarizable water is stable with 30 fs timestep
;
nsteps = 1000000
; number of steps for center of mass motion removal =
;nstcomm = 1
;comm-grps =
; OUTPUT CONTROL OPTIONS =
; Output frequency for coords (x), velocities (v) and forces (f) =
nstxout = 5000
nstvout = 5000
nstfout = 0
; Output frequency for energies to log file and energy file =
nstlog = 1000
nstenergy = 100
; Output frequency and precision for xtc file =
nstxtcout = 5000
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 = PW
; 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 = PME
coulombtype = shift
rcoulomb = 1.2
;
; Polarizable water may be used with standard Martini shift, but also with PME
;
rcoulomb_switch = 0.0
; Dielectric constant (DC) for cut-off or DC of reaction field =
epsilon_r = 2.5
; 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
; Spacing for the PME/PPPM FFT grid =
fourierspacing = 0.12
; FFT grid size, when a value is 0 fourierspacing will be used =
fourier_nx = 10
fourier_ny = 10
fourier_nz = 10
; EWALD/PME/PPPM parameters =
pme_order = 4
ewald_rtol = 1e-05
epsilon_surface = 0
optimize_fft = no
; OPTIONS FOR WEAK COUPLING ALGORITHMS =
; Temperature coupling =
tcoupl = Berendsen ; v-rescale
; Groups to couple separately =
tc-grps = system
; Time constant (ps) and reference temperature (K) =
tau_t = 0.3
ref_t = 300
; Pressure coupling =
Pcoupl = Berendsen ; Parrinello-Rahman
Pcoupltype = isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar) =
tau_p = 3.0
compressibility = 3e-5
ref_p = 1.0
; SIMULATED ANNEALING CONTROL =
annealing = no
; Time at which temperature should be zero (ps) =
zero_temp_time = 0
; GENERATE VELOCITIES FOR STARTUP RUN =
gen_vel = no
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
; Relative tolerance of shake =
shake_tol = 0.0001
; 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 = 90
;
; for polarizable water sometimes Lincs warnings appear for no apparent reason
; with a warnangle of 90 this is largely avoided