; e.g.: -I/home/joe/doe -I/home/mary/roe
include = -I/home/me/stuff
; e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive)
-define =
+define = -DBOOLVAR -DVAR=VALUE
; RUN CONTROL PARAMETERS
integrator = steep
init_step = 0
; Part index is updated automatically on checkpointing (keeps files separate)
simulation-part = 1
+; Multiple time-stepping
+mts = no
; mode for center of mass motion removal
comm-mode = Linear
; number of steps for center of mass motion removal
energygrps =
; NEIGHBORSEARCHING PARAMETERS
-; cut-off scheme (Verlet: particle based cut-offs, group: using charge groups)
+; cut-off scheme (Verlet: particle based cut-offs)
cutoff-scheme = Verlet
; nblist update frequency
nstlist = 10
-; ns algorithm (simple or grid)
-ns-type = Grid
; Periodic boundary conditions: xyz, no, xy
pbc = xyz
periodic-molecules = no
lj-pme-comb-rule = Geometric
ewald-geometry = 3d
epsilon-surface = 0
-
-; IMPLICIT SOLVENT ALGORITHM
-implicit-solvent = No
-
-; GENERALIZED BORN ELECTROSTATICS
-; Algorithm for calculating Born radii
-gb-algorithm = Still
-; Frequency of calculating the Born radii inside rlist
-nstgbradii = 1
-; Cutoff for Born radii calculation; the contribution from atoms
-; between rlist and rgbradii is updated every nstlist steps
-rgbradii = 1
-; Dielectric coefficient of the implicit solvent
-gb-epsilon-solvent = 80
-; Salt concentration in M for Generalized Born models
-gb-saltconc = 0
-; Scaling factors used in the OBC GB model. Default values are OBC(II)
-gb-obc-alpha = 1
-gb-obc-beta = 0.8
-gb-obc-gamma = 4.85
-gb-dielectric-offset = 0.009
-sa-algorithm = Ace-approximation
-; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA
-; The value -1 will set default value for Still/HCT/OBC GB-models.
-sa-surface-tension = -1
+implicit-solvent = no
; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
; OPTIONS FOR QMMM calculations
QMMM = no
-; Groups treated Quantum Mechanically
+; Groups treated with MiMiC
QMMM-grps =
-; QM method
-QMmethod =
-; QMMM scheme
-QMMMscheme = normal
-; QM basisset
-QMbasis =
-; QM charge
-QMcharge =
-; QM multiplicity
-QMmult =
-; Surface Hopping
-SH =
-; CAS space options
-CASorbitals =
-CASelectrons =
-SAon =
-SAoff =
-SAsteps =
-; Scale factor for MM charges
-MMChargeScaleFactor = 1
-; Optimization of QM subsystem
-bOPT =
-bTS =
; SIMULATED ANNEALING
; Type of annealing for each temperature group (no/single/periodic)
; COM PULLING
pull = no
+; AWH biasing
+awh = no
+
; ENFORCED ROTATION
; Enforced rotation: No or Yes
rotation = no
calc-lambda-neighbors = 1
init-lambda-weights =
dhdl-print-energy = no
+sc-function = beutler
sc-alpha = 0
sc-power = 1
sc-r-power = 6
sc-sigma = 0.3
sc-coul = no
+sc-gapsys-scale-linpoint-lj = 0.85
+sc-gapsys-scale-linpoint-q = 0.3
+sc-gapsys-sigma-lj = 0.3
separate-dhdl-file = yes
dhdl-derivatives = yes
dh_hist_size = 0
userreal2 = 0
userreal3 = 0
userreal4 = 0
+; Electric fields
+; Format for electric-field-x, etc. is: four real variables:
+; amplitude (V/nm), frequency omega (1/ps), time for the pulse peak (ps),
+; and sigma (ps) width of the pulse. Omega = 0 means static field,
+; sigma = 0 means no pulse, leaving the field to be a cosine function.
+electric-field-x = 0 0 0 0
+electric-field-y = 0 0 0 0
+electric-field-z = 0 0 0 0
+
+; Density guided simulation
+density-guided-simulation-active = false
+
+; QM/MM with CP2K
+qmmm-cp2k-active = false
</String>
</ReferenceData>