; RUN CONTROL PARAMETERS
integrator = md
; Start time and timestep in ps
tinit = 0
dt = 0.002
nsteps = 100000000
; For exact run continuation or redoing part of a run
init_step = 0
; 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 = 500
nstenergy = 500
; Output frequency and precision for xtc file
nstxout-compressed = 500
compressed-x-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 =
; NEIGHBORSEARCHING PARAMETERS
; cut-off scheme (Verlet: particle based cut-offs, group: using charge groups)
cutoff-scheme = Verlet
; nblist update frequency
nstlist = 10
; ns algorithm (simple or grid)
ns_type = grid
; Periodic boundary conditions: xyz (default), no (vacuum)
; or full (infinite systems only)
pbc = xyz
; nblist cut-off
rlist = 1.1
; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype = PME
rcoulomb-switch = 0
rcoulomb = 1.1
; Relative dielectric constant for the medium and the reaction field
epsilon-r = 1
epsilon_rf = 1
; Method for doing Van der Waals
vdw-type = Cut-off
; cut-off lengths
rvdw-switch = 0
rvdw = 1.1
; Apply long range dispersion corrections for Energy and Pressure
DispCorr = No
; Extension of the potential lookup tables beyond the cut-off
table-extension = 1
; Seperate tables between energy group pairs
energygrp_table =
; Spacing for the PME/PPPM FFT grid
fourierspacing = 0.12
; 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 = 4
ewald_rtol = 1e-05
ewald_geometry = 3d
epsilon_surface = 0
; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
Tcoupl = V-rescale
; Groups to couple separately
tc-grps = Protein Water_and_ions
; Time constant (ps) and reference temperature (K)
tau_t = 0.2 0.2
ref_t = 298 298
; Pressure coupling
Pcoupl = Parrinello-Rahman
Pcoupltype = Isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau-p = 1
compressibility = 4.5e-5
ref-p = 1
; GENERATE VELOCITIES FOR STARTUP RUN
gen_vel = no
gen_temp = 298
gen_seed = -1
; OPTIONS FOR BONDS
constraints = h-bonds
; Type of constraint algorithm
constraint-algorithm = Lincs
; Do not constrain the start configuration
unconstrained-start = no
; Use successive overrelaxation to reduce the number of shake iterations
Shake-SOR = no
; Relative tolerance of shake
shake-tol = 1e-04
; Highest order in the expansion of the constraint coupling matrix
lincs-order = 4
; Number of iterations in the final step of LINCS. 1 is fine for
; normal simulations, but use 2 to conserve energy in NVE runs.
; For energy minimization with constraints it should be 4 to 8.
lincs-iter = 1
; 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