;Preprocessing options
cpp=/usr/bin/cpp -traditional
include= -I../top
; define lambda for restraints, if appplicable
;define= -DPOSRES
; RUN CONTROL PARAMETERS =
integrator = md
; start time and timestep in ps =
tinit = 0
dt = 0.002
nsteps = 50000
; number of steps for center of mass motion removal =
nstcomm = 1
; OUTPUT CONTROL OPTIONS =
; Output frequency for coords (x), velocities (v) and forces (f) =
nstxout = 0
nstvout = 0
nstfout = 0
; Output frequency for energies to log file and energy file =
nstlog = 2000
nstenergy = 2000
; Output frequency and precision for xtc file =
nstxtcout = 2000
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 = Protein
; 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 = 1.0
domain-decomposition = no
; OPTIONS FOR ELECTROSTATICS AND VDW =
; Method for doing electrostatics =
coulombtype = pme
;rcoulomb-switch = 0
rcoulomb = 1.0
; Dielectric constant (DC) for cut-off or DC of reaction field =
epsilon-r = 1
; Method for doing Van der Waals =
vdw-type = Cut-off ;switch
; cut-off lengths =
;rvdw-switch = 0.8
rvdw = 1.0 ;0.9
; Apply long range dispersion corrections for Energy and Pressure =
DispCorr = EnerPres
; Spacing for the PME/PPPM FFT grid =
fourierspacing = 0.1
; FFT grid size, when a value is 0 fourierspacing will be used =
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
; EWALD/PME/PPPM parameters =
pme_order = 6
ewald_rtol = 1e-06
epsilon_surface = 0
optimize_fft = no
; Energy monitoring
energygrps = Protein SOL Na ;System
;OPTIONS FOR TEMPERATURE COUPLING
Tcoupl = nose-hoover ;nose-hoover
tc_grps = Protein Non-Protein
tau_t = 0.1 0.1
ref_t = 296.594 296.594
;OPTIONS FOR PRESSURE COUPLING
Pcoupl = No
tau_p = 0.5
compressibility = 4.5e-05
ref_p = 1.0
; GENERATE VELOCITIES FOR STARTUP RUN =
gen_vel = no
gen_temp = 296.594
gen_seed = -1
; OPTIONS FOR BONDS =
constraints = all-bonds ;hbonds
; Type of constraint algorithm =
constraint-algorithm = Lincs
; Do not constrain the start configuration =
unconstrained-start = yes ;no
; Relative tolerance of shake =
shake-tol = 0.0001
; Highest order in the expansion of the constraint coupling matrix =
lincs-order = 12
; Lincs will write a warning to the stderr if in one step a bond =
; rotates over more degrees than =
lincs-warnangle = 30
; Convert harmonic bonds to morse potentials =
morse = no