; RUN CONTROL PARAMETERS
integrator = sd
; Start time and timestep in ps
tinit = 0
dt = 0.002
nsteps = 30000000 ; the long simulation can be run by changing this time. you'll first try a short one and remember that it scales with sqrt(N)
; mode for center of mass motion removal
comm-mode = Linear
; number of steps for center of mass motion removal
nstcomm = 1
; ENERGY MINIMIZATION OPTIONS
; Force tolerance and initial step-size
emtol = 100
emstep = 0.01
; Max number of iterations in relax_shells
niter = 20
; Step size (1/ps^2) for minimization of flexible constraints
fcstep = 0
; Frequency of steepest descents steps when doing CG
nstcgsteep = 1000
nbfgscorr = 10
; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout = 0
nstvout = 0
nstfout = 0
; Checkpointing helps you continue after crashes
nstcheckpoint = 1000
; Output frequency for energies to log file and energy file
nstlog = 100
nstenergy = 100
; 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 = solut Water
; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist = 10 ;match Karisa
; 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 = 1.2
;domain-decomposition = no ; match Karisa
; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype = pme
rcoulomb-switch = 0
rcoulomb = 1.2
; Dielectric constant (DC) for cut-off or DC of reaction field
;epsilon-r = 1 ; match Karisa
; Method for doing Van der Waals
vdw-type = Switch
; cut-off lengths
rvdw-switch = 0.9
rvdw = 1.0
; Apply long range dispersion corrections for Energy and Pressure
;DispCorr = EnerPres ; Match Karisa
DispCorr = AllEnerPres
; Extension of the potential lookup tables beyond the cut-off
;table-extension = 1 ; match Karisa
; Spacing for the PME/PPPM FFT grid
;fourierspacing = 0.12
fourierspacing = 0.10 ; Match Karisa
; 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 ; Match Karisa
pme_order = 6
;ewald_rtol = 1e-05
ewald_rtol = 1e-06 ; Match Karisa
ewald_geometry = 3d
epsilon_surface = 0
;optimize_fft = no
optimize_fft = yes ; Match Karisa
; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
Tcoupl = no
; Groups to couple separately
tc-grps = System
; Time constant (ps) and reference temperature (K)
tau_t = 2.0
ref_t = 298.15
; Pressure coupling
Pcoupl = Parrinello-Rahman
Pcoupltype = isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau_p = 10
compressibility = 4.5e-5
ref_p = 1.01325
; Random seed for Andersen thermostat
andersen_seed = 815131
; GENERATE VELOCITIES FOR STARTUP RUN
gen_vel = no
;gen_temp = 298.15
;gen_seed = 1993
ld_seed = -1
; OPTIONS FOR BONDS
constraints = hbonds
; 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
lincs-order = 12 ; Match Karisa
; 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 = 2 ; Removed to Match Karisa
; 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
; ENERGY GROUP EXCLUSIONS
; Pairs of energy groups for which all non-bonded interactions are excluded
energygrp_excl =
; Free energy control stuff
free-energy = no
;init_lambda_state = XXX
;fep_lambdas = 0.0 0.25 0.5 0.75 1.0 1.00 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0
;vdw_lambdas = 0.0 0.00 0.0 0.00 0.0 0.05 0.1 0.2 0.3 0.4 0.5 0.6 0.65 0.7 0.75 0.8 0.85 0.9 0.95 1.0
;couple-moltype = MOL
;couple-lambda0 = vdw-q
;couple-lambda1 = none
;couple-intramol = no
;sc-alpha = 0.5
;sc-sigma = 0.3
;sc-power = 1.0
;sc-coul = no
;nstdhdl = 100
;calc-lambda-neighbors = -1