CAST.txt

####################################
#                                  #
#                                  #
#         CAST CONFIGFILE          #
#                                  #
#                                  #
####################################
#
# Lines beginning with a hashtag are ignored by CAST

# Verbosity
# Amount of output information from CAST [0-5] (do not use verbosity > 4)

verbosity              3

# Cores
# Number of OpenMP Threads (if compiled with openmp support)

cores                  4


####################################
#                                  #
#                                  #
#        I/O: FILES & TYPES        #
#                                  #
#                                  #
####################################

# Input file name

name                   octane.arc

# Output file name

outname                output

# Input file type

inputtype              TINKER

### AMBER I/O OPTIONS

#amber_mdcrd
#amber_mdvel
#amber_inpcrd
#amber_restrt           min2.rst
#amber_trajectory_at_constant_pressure

### XYZ I/O OPTIONS

# try to create oplsaa atomtypes from amino acids
#xyz_atomtypes           1


####################################
#                                  #
#          PROGRAM TASK            #
#                                  #
####################################

# SP                    Single point eneryg calculation
# GRAD                  Single point gradient calculation
# HESS                  Single point hessian matrix calculation
# LOCOPT                Local optimization using Lib-LBFGS
# GOSOL                 Combined Solvation + Global Optimization
# MC                    Monte Carlo
# TS                    Tabu Search (CAST: GOTS)
# DIMER                 Dimer method using torsional space
# MD                    Molecular dynamics simulation
# NEB                   Nudged elastic band calculation
# STARTOPT              Adding water molecules and / or performing Ringsearch
# UMBRELLA              Umbrella Sampling
# PMF_IC_PREP           Preparation task for enhanced umbrella sampling (PMF_IC)
# FEP                   Alchemical transformations using FEP
# ALIGN                 Trajectory Alignment (Kabsch algorithm)
# PCAgen                Principal Component Analysis
# PCAproc
# ENTROPY               Configurational and Conformational Entropy Calculations
# GRID                  Grid Search
# PATHOPT               Global reaction path search by constraint optimization on n-1 dim. hyperplane(s)
# PATHSAMPLING
# REMOVE_EXPLICIT_WATER
# WRITE_TINKER          Writes tinkerstructure into outname.arc
# WRITE_XYZ             Writes inputstructure in xyz-file outname.xyz
# WRITE_PDB             Writes inputstructure into .pdb file that can be opened in Pymol (especially useful for protein structures)
# WRITE_GAUSSVIEW       Writes inputstructure into .gjf file you can open with gaussview (useful to create QM/MM input)
# MOVE_TO_ORIGIN        Moves inputstructure to origin of coordinate system (0,0,0)
# FIND_AS               Gives a list of aminoacids and molecules with belonging atoms
# MODIFY_SK_FILES       Modifies slater koster files form dftb.org into the format needed by gaussian
# INTERNAL              Create Z-Matrix
# SCAN2D
# XB_CENTER             Center of mass/geometry
# XB_EXCITON_BREAKUP    Simulation of excitons at an semiconductor interface
# XB_INTERFACE_CREATION Combinig two structures
# XB_COUPLINGS          Calculation of couplings for XB_EXCITON_BREAKUP
# LAYER_DEPOSITION      Simulation of layerdeposition to construct a structure
# EXCITONDIMER
# XB_CENTER             Center of mass/geometry
# GET_MONOMERS          Get Monomerstructres from a structure

task                  SP


####################################
#                                  #
#        ENERGY INTERFACES         #
#                                  #
####################################

# AMBER                AMBER force field
# AMOEBA               AMOEBA03 force field
# CHARMM22             CHARMM22 force field
# OPLSAA               OPLS all atoms force field
# TERACHEM             Terachem MPI Interface
# MOPAC                MOAPC syscall Interface
# DFTB                 Interface to DFTB+
# DFTBABY              DFTBaby interface
# GAUSSIAN             GAUSSIAN interface 
# CHEMSHELL            under developement
# PSI4                 interface to PSI4
# ORCA                 interface to ORCA
# QMMM_A               (additive) QM/MM interface
# QMMM_S               (subtractive) QM/MM interface
# THREE_LAYER          three-layer interface (analogous to subtractive QM/MM)

interface              CHARMM22

# Interface for preoptimizations
#preinterface           OPLSAA

# PARAMETER FILE FOR FF
# paramfile            amber.prm, amoeba.prm, oplsaa.prm, charmm22.prm
paramfile              charmm22.prm

#Cutoff radius for non bonded interactions for forcefields energy interfaces
#cutoff                 12.0
#Radius to start switching function to kick in; scales interactions smoothly to zero at cutoff radius
#switchdist             10.0

# reading atom charges from separate file (called charges.txt) <0/1>,
# necessary for reproducing AMBER forefields accuratly
#chargefile             1

# Spackman correction
#Spackman 1 1 10.0

################## QM/MM OPTIONS ####################

# indices of QM atoms (add more lines for several QM systems - only subtractive QM/MM)
QMMMqmatoms           6,9,10,11,12,13,14,15
QMMMmminterface       OPLSAA
QMMMqminterface       DFTB

# write tinkerstructure of QM region into file? <0/1>
QMMMwriteqmintofile   1

# energy types of link atoms in forcefield, seperated by comma (in the order of QM atom)
# if three-layer: for middle system
# if subtractive QM/MM: add more lines for several QM systems
QMMMlinkatomtype      85, 85, 221

# cutoff for electrostatic interaction
#QMMMcutoff            10

# atom which defines center of QM region for cutoff (needs to be a QM atom)
# if three-layer: center of middle system
# give 0 if you want CAST to find the QM atom that is nearest to geometrical center of QM region
# if subtractive QM/MM: add more lines for several QM systems
QMMMcenter             0

# for atoms that are seperated from the inner region by a maximum of ... bonds the charges are set to zero for electronic embedding (available options: 0, 1, 2 or 3; where 0 means mechanical embedding)
QMMMzerocharge_bonds   1

# perform optimization with microiterations? <0/1>
# only available in subtractive QM/MM
QMMMopt                1

# convergence criterion for optimization with microiterations
QMMMconTol             0.1

# maximum number of outer cycles in optimization
QMMMmaxCycle           100

# use adjustment for coulomb interactions in MM calculation (0 = none, 1 = QM charges as parameters)
QMMMadjust             1

# write structure for each microiteration cycle into file? <0/1>
QMMMwrite_opt          1


# for THREE_LAYER only:

QMMMseatoms           52-54
QMMMseinterface       DFTB

# include MM charges in QM system (0=EEx, 1=EE in Gaussian, 2=EE+, 3=EE+X)
QMMMsmall_charges     1

# atom which defines center of small region for cutoff (only relevant for EE+ and MMSE)
QMMMsmall_center      0


######################### MOPAC OPTIONS ###############

# Keywords for MOPAC Call 
MOPACkey               PM7

# Delete temporary MOPAC comm files?
MOPACdelete            0

#MOPAC executable path
MOPACpath              /apps/mopac/MOPAC2016.exe

MOPACversion           MOPAC2016

# total charge of system 
MOPACcharge            0


############################ GAUSSIAN OPTIONS ########################

GAUSSIANlink NProcShared=4 Mem=4GB

# Name of Gaussian checkpoint file
#GAUSSIANchk     OPT.chk

#Methods for Gaussian Call

GAUSSIANmethod HF

#Basisset for Gaussian Call

GAUSSIANbasisset 6-31G

#Further specifications for Gaussian Call

#GAUSSIANspecifications

#Charge of the Molecule

GAUSSIANcharge 0

#Multiplicity

GAUSSIANmultiplicity 1

#Use of gaussian optimizer

GAUSSIANopt   1

#Gaussian optimization with steepest descend

GAUSSIANsteep 0

#Gaussian executeable path

GAUSSIANpath g16

#Delete temporary Gaussian f i l e s ?

GAUSSIANdelete 0

#Number of failed gaussian calls when CAST breaks

GAUSSIANmaxfail      1000

###### stuff for implicit solvent ######

# use conductor-like polarizable continuum model (CPCM) <0/1>
GAUSSIANcpcm        0

# dielectric constant 
#GAUSSIANeps         2.0

# dynamic dielectric constant (might be square of refractive index)
#GAUSSIANepsinf      1.0


################## ORCA OPTIONS #################################################

# path to ORCA
ORCApath      /apps/orca/4.1.1/ORCA/orca

# number of processors used
ORCAnproc     1

# maximum amount of scratch memory per core (in MB)
ORCAmaxcore   1000

# method for ORCA
ORCAmethod    HF

# basisset for ORCA
ORCAbasisset   6-31G

# further specifications for ORCA call (written in line with method and basisset)
#ORCAspec       bla

# charge of the molecule
ORCAcharge     0

# multiplicity of the molecule
ORCAmultiplicity   1

# which optimizer should be used? (0=CAST, 1=ORCA)
ORCAopt        1

# verbosity for ORCA (0 - 5)
ORCAverbose     1

# orbitals that should be plotted as cubefiles
#ORCAcube        56-63

###### stuff for casscf calculations ######

# add casscf section to inputfile <0/1>
ORCAcasscf      0

# number of electrons
ORCAnelec       2

# number of orbitals
ORCAnorb        4

# number of roots
ORCAnroots      1

# use Newton-Raphson algorithm <0/1>
ORCAnr          1

# switch on NEVPT2 <0/1>
ORCAnevpt       1

###### stuff for implicit solvent ######

# use conductor-like polarizable continuum model (CPCM) <0/1>
ORCAcpcm        0

# dielectric constant 
ORCAeps         2.0

# refractive index
ORCArefrac      1.0


################# DFTB+ Options #################################################

# path to DFTB+
DFTB+path         /apps/dftbplus/bin/dftb+

# path to slater koster files (download at https://www.dftb.org/parameters/download/)
DFTB+skfiles      /apps/dftbplus/3ob-3-1/

# verbosity of DFTB+
DFTB+verbose      1

# convergence tolerence for SCC procedure (raise for calcualation for hessian matrix)
DFTB+scctol       0.00001

# maximum number of steps for SCC procedure
DFTB+max_steps_scc   1000

# total charge of the system
DFTB+charge      0

# use DFTB3 <0/1>
DFTB+3           1

# use D3 correction? <0/1>
DFTB+D3          1

# which parameters for D3 correction should be used?
# (0 = 3OB, 1 = OB2(base), 2 = OB2(shift), 3 = OB2(split))
DFTB+D3param     1

# use range-separation? <0/1>
DFTB+range_sep   0

# temperature for fermi filling (in K)
#DFTB+fermi_temp       300

# optimizer (0 = CAST, 1 = Steepest Decent, 2 = Conjugate Gradient)
DFTB+optimizer    2

# maximum number of steps for optimization with DFTB+ optimizer
DFTB+max_steps_opt    5000


################# PSI4 options ###################################################

# command to execute psi4
PSI4-path             /apps/psi4/psi4

# reserve memory
PSI4-memory           4GB

# basisset for calculation
PSI4-basis            6-31G

# method for calculation
PSI4-method           HF

# spin multiplicity for molecule
PSI4-spin             1

# charge of molecule
PSI4-charge           0

# number of threads
PSI4-threads          4


################# DFTBaby options ################################################

# path to DFTBaby
DFTBath                 /home/susanne/DFTBaby-0.1.0

# verbosity (only for DFTBaby)
DFTBverbose             0

# total charge of molecule (has to be closed shell)
#DFTBcharge              0

# distance cutoff (in bohr): orbitals whose centers are further away than this cutoff do not interact
#DFTBcutoff            30

# switch on long range correction <0/1>
DFTBlr_corr             1

# distance (in bohr) where the long range correction is switched on
DFTBlr_dist            3.03

# maximum number of iterations for SCF-calculation
#DFTBmaxiter            1000

# convergence threshold for relative change in SCF-calculation
#DFTBconv               1e-10

# name of the DFTBaby gradient file
DFTBgradfile            grad.xyz

# state for which the DFTB gradients should be calculated (ground state = 0)
DFTBgradstate          0

# limit the TD-DFTB matrix (used for gradients) to the lowest ... eigenvalues
DFTBstates            1

# number of occupied orbitals taken into account for TD-DFTB
DFTBocc_orb            2

# number of virtual orbitals taken into account for TD-DFTB
DFTBvirt_orb            2

# maximum number of iterations for TD-DFTB matrix diagonalisation
#DFTBdiag_maxiter        50

# convergence threshold for TD-DFTB matrix diagonalisation
#DFTBdiag_conv           1e-05

# use DFTBaby for optimization (otherwise steepest gradient) <0/1>
DFTBopt                  0

################### CHEMSHELL OPTIONS #########################

CHEMSHELL-path /apt/chemshell

CHEMSHELL-scheme shift

CHEMSHELL-qm_theory turbomole

CHEMSHELL-qm_hamiltonian b3lyp

CHEMSHELL-qm_basisset def-TZVP

CHEMSHELL-qm_charge 0

CHEMSHELL-qm_atoms 337 - 341 2269 - 2279 32426 - 32428

CHEMSHELL-residues CYS25 HIE162 WAT10006

CHEMSHELL-delete 0

####################################
#                                  #
#        MOVE TO ORIGIN            #
#                                  #
####################################

# 1: move to center of geometry
# 2: move to center of mass

#MOVEmode            1


####################################
#                                  #
#             FIND AS              #
#                                  #
####################################

# use output of FIND_AS as input for MDregions? <0/1>
FIND_AS_mdRegions      1


####################################
#                                  #
#          ATOM FIXATIONS          #
#                                  #
####################################

# Exclude nonbondeds between two fixed atoms in internal force fields
FIXexclude             false

# Remove rotations of hydrogens from main torsional angles
REMOVEHROT             false

# Fix a range of atoms (indizes in tinker numbering, i.e. starting with 1)
#FIXrange               1-6,9,24,55-71,72

# fix all atoms outside a sphere around a given atom (first number is atom, second number is sphere radius)
#FIXsphere               1    13.0

####################################
#                                  #
#              BIASES              #
#                                  #
####################################

# Spherical Bias Potential 
#BIASspherical                <radius> <force> <exponent>
#BIASspherical                   25.0    1.0      2.0

# Cubic Bias Potential
#BIAScubic                    <x> <y> <z> <force> <exponent>
#BIAScubic                   40.0 40.0 40.0 1.0      2.0

# Quadratic Dihedral Bias Potential (quadratic in degreees)
#BIASdih                <atom 1> <atom 2> <atom 3> <atom 4> <angle> <force>
#BIASdih                   1        2        3         5       0.0   10.0
#BIASdih                   2        5        6         9     150.0    5.0

# Harmonic Distance Bias Potential (in angstrom)
#BIASdist               <atom 1> <atom 2> <angstrom> <force>

# Harmonic angle bias potential (in degree)
#BIASangle            <atom 1> <atom 2> <atom 3> <angle> <force>
#BIASangle             2          1        3      90.0    500.00  


####################################
#                                  #
#             MAINlists            #
#                                  #
####################################

# Black- or Whitelist a rotation around a bond
# for the selection as main rotation

#MAINblacklist 2 5

#MAINwhitelist 2 5


####################################
#                                  #
#       Periodic Boundaries        #
#                                  #
####################################

#Periodics            <Active 1(on)/0(off)> <box-x> <box-y> <box-z>
#Periodics              0 70.0 70.0 70.0

# Print periodic boundary dummy atoms to output?
#Periodicp            <Active 1(on)/0(off)>

#Periodicp              0

# Periodic Cutoout: Cut out all molecules that are not in periodic boundry box
PeriodicCutout false
# 0: Remove entire molecule if any atom of molecule is outside box + CutoutDistance
# 1: Remove entire molecule if center of mass is outside box + CutoutDistance
PeriodicCutoutCriterion 1
# Additional CutoutDistance from box edge in angstrom , where molecules are cut
PeriodicCutoutDistance 0

IsotropicPeriodics     0 #If barostat is used this option can turn on isotripic behaviour

####################################
#                                  #
#         LOCOPT OPTIONS           #
#                                  #
####################################

# which optimizer to use? (1 = L-BFGS, 2 = INTERNAL, 3 = OPT++)
OPTimizer             2

should trace be written into file? <0/1>
OPTtrace              0


### OPTIONS FOR L-BGFS ###

# convergence threshold for bfgs
OPTconTol             0.001

#max number of steps for bfgs
OPTmaxstep            5000

# use same convergence criterion as for QM/MM opt? <0/1>
OPTconvergenceCriterion  0

### OPTIONS FOR INTERNAL ###

# all those options are for setting constraints

# constrain all...
OPTconstraint_bond_lengths       false
OPTconstraint_bond_angles        false
OPTconstraint_dihedrals          false
OPTconstraint_out_of_plane_bends false
OPTconstraint_translations       false
OPTconstraint_rotations          false

# Constrain individual coordinates (not supported for out-of-plane bends):
# constraint_coordinate <bond|ang|dih|trans[X|Y|Z]|Rot[A|B|C]> AtomA AtomB [AtomC [AtomD [...]]] [freeze|unfreeze]
# "bond" and 2 Atoms given --> Bond length
# "ang" and 3 Atoms given --> Bond angle
# "dih" and 4 Atoms given --> Dihedral angle
# "transX" and an arbitrary number of Atoms given --> Translation in X-direction
# "transY" and an arbitrary number of Atoms given --> Translation in Y-direction
# "transZ" and an arbitrary number of Atoms given --> Translation in Z-direction
# "rotA" and an arbitrary number of Atoms given --> Rotation around A
# "rotB" and an arbitrary number of Atoms given --> Rotation around B
# "rotC" and an arbitrary number of Atoms given --> Rotation around C
# Duplicate atoms are ignored. If nothing stands behind the list of atoms this 
# coordinate is frozen. If there stands anything except "freeze" it is unfrozen.
# Note that you do not need to write unfreeze specifically, anything counts as unfreezing.
# Multiply defined constraints are added multiple times.

# Examples:
# Free bond length between atoms 1 and 3
# OPTconstraint_coordinate bond 1 3 unfreeze

# Fix bond angle between atoms 1, 4 and 5
# OPTconstraint_coordinate 1 4 5 freeze


### OPTIONS FOR OPT++

# which optimizer to use? (0 = QNIPS, 1 = FDNIPS)
OPT++imizer                0

# function tolerance       
OPT++fcnTol                0.000001

# gradient tolerance       
OPT++gradTol               0.0001

# step tolerance
OPT++stepTol               0.000000001

# maximum number of iterations
OPT++maxIter               5000

# maximum number of function evaluations
OPT++maxFeval              10000

# linesearch tolerance
OPT++lsTol                 0.0001

# maximum number of iterations in linesearch
OPT++maxBacktrackIter      1000

# minimal step size
OPT++minStep               0.0000000001

# maximum step size
OPT++maxStep               10

# merit function
# 0 = NormFmu, 1 = ArgaezTapia, 2 = VanShanno
OPT++meritFcn              1

# constraint bond (maximum two constraints possible)
# given like this: <index1> <index2> <dist>
#OPT++constraint_bond       1  100  6.02
#OPT++constraint_bond       29  55  4.12

# hard constraint tolerance (only for QNIPS)
OPT++constraintTol              0.001


###################################
#				  #
#      NEB & PATHOPT OPTIONS      #
#				  #
###################################

# Second structure for double-ended search
NEB-PATHOPT-FINAL input.xyz

# Number of NEB images
NEB-PATHOPT-IMAGES 12

# Force constant in kcal/molA^2 for NEB calculation defining the force component along the connecting band
NEB-PATHOPT-SPRING 1.0

# Climbing image in NEB 0/1 (off/on)
NEB-PATHOPT-CLIMBING 1

# Standard tau or improved tau method in NEB 0/1 (standard/improved)
NEB-PATHOPT-TAU 1

# Definition of the Temperature settings for the Monte Carlo run
NEB-PATHOPT-TEMP 298.15

# MCM iterations in Pathopt
NEB-PATHOPT-ITER 60

# Number of multiple MCM simulations
NEB-PATHOPT-GLOBITER 1

# Optimization mode BIAS/GRADIENT Projection
NEB-PATHOPT-MODE PROJECTED

# Bias constant (Pathopt)
NEB-PATHOPT-BIASCONSTANT 0.1

# Maximum displacement in Angstrom for accepted coordinates in MCM
NEB-PATHOPT-MAXVAR 3.0

# Maximum energy range in kcal/mol for MCM in Pathopt
NEB-PATHOPT-ENERGY_RANGE 20.0

# MCM stepsize in Angstrom
NEB-PATHOPT-STEPSIZE 1.4

# Move strategy by applying dihedral changes at several steps of MCM 0/1 (off/on)
NEB-PATHOPT-MIXMOVE 0

# Using NEB connection within Pathopt 0/1 (off/on)
NEB-PATHOPT-NEBCONN 0

# Number of NEB images within Pathopt-NEB connection procedure
NEB-PATHOPT-NUMBER_NEBCONN 12

# Constraint global optimization (MCM standard) by fixation of
# dihedrals which change the most during NEB
NEB-PATHOPT-CONSTRAINT_GLOBAL 0

# Number of dihedrals within constraint global optimization
# (MCM standard) which should be fixed along the NEB path
NEB-PATHOPT-CONSTRAINT_NUMBER_DIHEDRALS 1

NEB-PATHOPT-BOND_PARAM   2.2

# Interpolation via spline method between the linear constructed NEB pathway
# by locally optimizing with perpendicular force projection 0/1 (off/on)
NEB-PATHOPT-INT_PATH 0

#step size of interpolated images via spline interpolation approach
NEB-PATHOPT-INT_IT 0.5

#choose if the MaxFlux method is used to simulate a NEB method with temperature dependencies (0/1 no/yes)
NEB-PATHOPT-MAXFLUX 1

#determine if a neb calculation is performed for every found path in PATHOPT (0/1: no/yes)
NEB-PATHOPT-MF_PATHOPT 1

#using image dependent pair potential (IDPP) for NEB pathway generation (0/1: no/yes)
NEB-PATHOPT-NEB-IDPP 1

#usin complete pathway (multiple structure file) for NEB calculation (0/1: no/yes)
NEB-PATHOPT-NEB-COMPLETE 1

#complete pathways or points with interconnection via NEB (0/1: no/yes)
NEB-PATHOPT-NEB-MULTIPLE_POINTS 0

NEB-PATHOPT-NEB-INTERNAL_INTERPOLATION   0

NEB-PATHOPT-NEB-MCM_OPT     1

NEB-PATHOPT-NEB-MC_SAVE     1

NEB-PATHOPT-CONN            1

####################################
#                                  #
#          SCAN2D OPTIONS          #
#                                  #
####################################

# this is how to define the scanpoints
# you need to give two of these lines
#2DSCAN-bond <index1> <index2> <start> <stop> <number of steps>
#2DSCAN-angle <index1> <index2> <index3> <start> <stop> <number of steps>
#2DSCAN-dihedral <index1> <index2> <index3> <index4> <start> <stop> <number of steps>

2DSCAN-dihedral 1 2 6 9 -180 180 73
2DSCAN-dihedral 12 15 18 21 -180 180 73

# setting down verbosity during scan? <0/1>
2DSCAN-verboseoff  1

# should fixed scan be performed? 
# (only recommended for debugging purposes)
2DSCAN-fixed_scan  0

# after constraint optimization perform a second optimization where the atoms forming the constraints are fixed (only for OPT++ optimizer)
2DSCAN-postopt_fixAtoms    0

####################################
#                                  #
#        SIMULATION OPTIONS        #
#            (MC, TS)              #
#                                  #
####################################

# Simulation Temperature
# for TS and MC important for Metropolis Criterion

Temperature            298.15

# Number of iterations in global optimization routine

Iterations             2000


####################################
#                                  #
#           GLOBOPTIONS            #
#            (MC, TS)              #
#                                  #
####################################

# Save all (minimized) structures
# which are within "Erange" kcal/mol from the final global minimum
# default = 0.0

GOerange                 10.0

# use the current local minimum energy for metropolis criterion?
# default = 0

GOmetrolocal           0

# startopt before starting simulation/optimization?
# default = 0

GOstartopt             0

# Temperature Scaling Factor applied to the Temperature,
# once a new minimum is found during GlobOpt
# default = 1.0

Tempscale              0.98

# Precision of values printed

GOprecision            6

# Fallback type
#
# LAST_GLOBAL (default) = fall back to last minimum and then to global minimum if stuck
# EVOLUTION = select new minimum via evolutionary algorithm if stuck

GOfallback             FITNESS_ROULETTE

# Maximum number of tries from one structure before it is set
# tabu as a starting point
# default = 20

GOfallback_limit       500

# Fitness function type for evolutionary fallback
#
# LINEAR (default) = linear ranking
# EXPONENTIAL = exponential ranking

GOfallback_fr_fit              EXPONENTIAL

# Number of minima included in the ranking for evolutionary fallback
# default = 10

GOfallback_fr_minima    10

# Lower and upper bounardy for fitness value
# rank 1 is assign second value, rank X
# (determined via GOincluded_minima) is assigned the first value
# default = 0.5 1.0

GOfallback_fr_bounds       0.5 1.0


####################################
#                                  #
#           GRID OPTIONS           #
#                                  #
####################################

GOmain_grid            60.0


####################################
#                                  #
#            MCM OPTIONS           #
#                                  #
####################################

# Step size in cartesian space

MCstep_size            1.4

# Use minimization

MCminimization         1

# Use dihedral (1), cartesian (2) or biased dihedral (0) randomization

MCmovetype             1

# Maximum dihedral deviation

MCmax_dihedral         30.0


####################################
#                                  #
#            TS OPTIONS            #
#                                  #
####################################

# Do diversification before first TS steps?

TSmc_first             1

# How many TS steps need to fail in finding new minimum before diversification?

TSdivers_threshold      10

# How many diversification steps are applied?

TSdivers_iter          30

# How often will diversification be applied before termination?

TSdivers_limit         20


####################################
#                                  #
#         STARTOPT OPTIONS         #
#                                  #
####################################

# startopt type
# 0                  Ringsearch
# 1                  Solvadd [default]
# 2                  Ringsearch + Solvadd

SOtype                 1

# startopt structure count
# number of structures generated by startopt routines

SOstructures           1


####################################
#                                  #
#        RINGSEARCH OPTIONS        #
#                                  #
####################################

# Force, applied to close rings
# (multiplied with quadratic in degrees of dihedral deviation)

RSbias_force           10.0

# Chance to close a ring in the initial random population generation

RSchance_close         0.33

# Number of individuals in the ringsearch evolution

RSpopulation           10

# Number of propagated generations during ringsearch evolution

RSgenerations          10


####################################
#                                  #
#          SOLVADD OPTIONS         #
#                                  #
####################################

# Hydrogen bond length parameter [default: 1.8]

SAhb                   1.8

# number of desired water molecules [default: 0(=no limit)]

#SAlimit                20

# water boundary type
#
# 0    layer [default]
# 1    sphere
# 2    box

SAboundary             2

# water boundary extent [default: 10.0] and push length (elongation of radius if limit is not reached)

SAradius               40.0

# force field parameter types of oxygen and hydrogen
#
# 53 54   OPLS-AA
# 101 88   CHARMM
# 2001 2002  AMBER

SAtypes                53 54

# Intermediate optimizations
#
# 0    none
# 1    each "shell"
# 2    all waters
# 3    1+2

SAopt                  3

# fix initial structure <0/1>

SAfixinit              0


####################################
#                                  #
#            MD OPTIONS            #
#                                  #
####################################

# Number of Steps

MDsteps                1000

# Integrator
#
# 0                    Velocity-Verlet
# 1                    Beeman

MDintegrator           0

# Velocity Scaling

MDveloscale            1

# temperature control <0/1>
# (direct velocity scaling and Nose-Hoover only work if this option is activated)

MDtemp_control         1

# Thermostat (Nose-Hoover)

MDthermostat           1

#Scalingfactor for Nose-Hoover Thermostat (default value 0.1)

MDnosehoover_Q         0.1

# Timestep in picoseconds

MDtimestep             0.001

# start MD again from beginning if molecule gets destroyed

MDrestart_if_broken    0

# Activate Tracking (Log and Snapshots)

MDtrack                1

#MDtrackoffset         0

#
#   Snapshots
#

# Number
MDsnap                 1000
# Buffer size
MDsnap_buffer          100
# Optimize snapshots
MDsnap_opt             0

# Heating process control
#
# MDheat               <step> <temperature at that step>
# MDheat               2000   293.15

MDheat                 0  300

# Pressure control

#MDpress               0

#MDpcompress
#MDpdelay
#MDptarget

# Rattle constraints

# 0                    No Constraints
# 1                    All Hydrogen Bonds
# 2                    Specific Bonds

MDrattle               0

# use paramfile to get distance, can't be used when distances between non-bound atoms are constrained
MDrattle_use_paramfile   1

# Rattle bond specification
#
# MDrattlebond         <index1> <index2>

MDrattlebond             19 21

#distance for rattlebonds (only for MDrattle=2)
#MDrattledist           1
#MDrattledist           3

# Iteration offset for restart files

MDrestart_offset       10000

# Iteration offset for building up non-bonded pairlist

MDrefine_offset        100

# Resume simulation from restart file?

MDresume               0

# Optimize structure before starting of MD simulation? <0/1>

#MDpre_optimize


########################### ANALYZING MD SIMULATIONS #################

# the distances between these atoms are to be plotted during MD simulation

#MDana_pair         1,2
#MDana_pair         7,13
#MDana_pair         5,9

# analyze temperature in different zones around active site <0/1>
# (active site defined by MDactive site)

#MDanalyze_zones    1

#atom number(s) of active site <every atom a new line>
#MDactive_site        14

# zone width (Angstrom)
#MDzonewidth        1

#MDregion      first_region      1,2,3
#MDregion      second_region     5,6,7


####################################
#                                  #
#            FEP OPTIONS           #
#                                  #
####################################

FEPlambda      1.0
FEPdlambda     0.1
FEPvdwcouple   1.0
FEPeleccouple  0.5
FEPvshift      0.5
FEPcshift      0.0
FEPequil       1
FEPsteps       5
FEPfreq        1
FEPanalyze     0
FEPbar         1


####################################
#                                  #
#            PATH OPTIONS          #
#                                  #
####################################

# File containing the desired path end

PRendfile              PATHREL_END.xyz

# Maximum Energy distance within the path

PRdeltae               0.5

# Maximum structure distance with the path

PRdeltax               0.5


####################################
#                                  #
#           DIMER OPTIONS          #
#                                  #
####################################
#
# Distance between dimer start end endpoint

DIMERdistance          0.001

# Maximum absolute of rotational force during dimer translation

DIMERtflimit           0.01

# Convergence criterion for the dimer rotation

DIMERrotconvergence    5.0

# Maximum number of rotation and translation iterations

DIMERmaxit             50 250



####################################
#                                  #
#         UMBRELLA SAMPLING        #
#                                  #
####################################

# use umbrella combination biases also for other tasks than UMBRELLA
USuse                  0

# number of equilibration steps
USequil                100

# definition of strained torsion 

#UStorsion              <index 1> <index 2> <index 3> <index 4> <force> <value>
#UStorsion              2 3 4 5  0.05   80.0

# definition of a strained angle

#USangle            <atom 1> <atom 2> <atom 3> <force> <value>
#USangle             2          1        3       1000.0    90.00  

# definition of strained distance

#USdist                 <index 1> <index 2> <force> <value>
#USdist                 1 2 1000.0 1.09
#USdist                 4 3 1000.0 3.0

# definition of combination of strained distances

#UScomb       <number of dists> <force> <value> ( <index1> <index2> <factor> ) 
# for every distance: another ( <index1> <index2> <factor> ) 
#UScomb        2  100000 0  ( 1  2  +1 ) (  1  6  -1 )


# Offset for taking snapshots
USsnap        1

############################# PMF IC ###################################

# variables for calculating z
US_xi0         0.0, 0.0
US_L           90.0, 90.0

# low level method (only relevant for PMF_IC_PREP)
US_methodLL    DFTB

# atom indices for bias (only one bias possible, should be identical to strained stuff above)
US_indices     2 3 4 5
US_indices     4 5 6 7

# range in which spline should be plotted in PMF_IC_PREP <start, stop, step>
US_range       -180  180  1
US_range       -180  180  1

# number of gridpoints for 2D spline
US_2d_gridpoints  73, 73

# nonlinearity penalty for 2D spline
US_2d_penalty    0.1

# use PMF_IC for umbrella-task? <0/1>
US_PMF_IC      1

# name of the file where the spline is created from
US_prepfile    output_PMF_IC.csv

####################################
#                                  #
#        XB_EXCITON_BREAKUP        #
#                                  #
####################################

#Center of masses of all semiconductor molecules

EXmasscenters           CenterofMasses.out

#Numbers of monomers

EXnumbern               60

EXnumberp               80

#Orientation of the interface

EXplaneinterf            z

#Minimum requzired startingpoints

EXminNbrStartingpoints     10

#Start Scaling factor for startingpoint search

EXstartingPscaling 0.86

#Number of steps in MC calculation

EXnumberofsteps          100000

#transition rates for all possible dimers

EXcouplings                   Couplings.txt

EXnscpairrates              nSC_homodimer.txt

EXpscpairexrates            homodimer_exciton.txt

EXpscpairchrates            homodimer_ladung.txt

EXpnscpairrates             heterodimer.txt

EXReorgE_exc                0.561

EXReorgE_ch                 0.194

EXReorgE_nSC                0.178

EXReorgE_ct                 0.156

EXReorgE_rek                0.184

EXct_triebkraft             1.550

EXrek_triebkraft           -4.913

EXoscillatorstrength        0.0852

EXwellenzahl                28514.9


####################################
#                                  #
#      XB_Interface Creation       #           
#                                  #
####################################

#Creation of a new Structure from the usual input structure and an additional one

#Additional input file name

ICname                     pyrene_dim.xyz

#Additional input file type

ICinputtype                TINKER

#From which axis should tha additional atoms added

ICaxis                      x

#How far apart should they be

ICdistance               8.0


####################################
#                                  #
#             XB_CENTER            #
#                                  #
####################################

CENTERdimer                     1

CENTERdistance                  15.0


####################################
#                                  #
#           XB_Couplings           #
#                                  #
####################################

#Number of p-type semiconductor monomers

CouplingspSCnumber              80

#Number of n-type semiconductor monomers         

CouplingsnSCnumber              60

#List of states relevant for ct-processes (no commata)

CouplingsCTcharastates          3 4 7

###p-type homodimer options

CouplingspSCdimMultiplicity          1

CouplingspSCdimCharge                0

CouplingspSCdimElCalcmethod          INDO

CouplingspSCdimExciCalcmethod        ZINDO TD=(NStates=9, Singlets,AllTransitiondensities) gfinput IOP(6/7=3)

###n-type homodimer options

CouplingsnSCdimMultiplicity          1

CouplingsnSCdimCharge                0

CouplingsnSCdimholCalcmethod         INDO

###heterodimer options

CouplingsheterodimMultiplicity       1

CouplingsheterodimCharge             0

CouplingsheterodimCalcmethod ZINDO TD=(NStates=9, Singlets,AllTransitiondensities) gfinput IOP(6/7=3)

####################################
#                                  #
#         LAYER_DEPOSITION         #
#                                  #
####################################

#Number of layers

LayDlayers                     4

#Number of molecules deleted per layer

LayDdel_number                 8

#From which axis should the layers be added

LayDaxis                       z 

#How far apart should they be

LayDdistance                   10.0

#Thresholdpotential fror layerdeposition  <distance from which active> <force constant [kcal/A]>
#thresholdpotential    18.0 10.0
#thresholdpotentialBottom    18.0 10.0

#Shall layers of a second moleculetype be added

LayDhet_struc                   1

LayDhet_name                    ful26_tinker_planey_newCenterXYplane.xyz

LayDhet_distance                8.0

LayDhet_layers                  4

LayDhet_del_number              8

#Shall monomers be replaced

LayDreplace                     0

LayDreference1                  dip.xyz

LayDreference2                  fullerene.xyz

####################################
#                                  #
#              ADJUST              #
#                                  #
####################################


#ADJUSTdih 1 2 3 4 180.0
#ADJUSTdih 2 3 4 5 180.0


####################################
#                                  #
#   TRAJECTORY ALIGNMENT OPTIONS   #
#                                  #
####################################

# Should alignment be performed?
traj_align_bool                true
# Should distance meassures be calculated and printed?
traj_print_bool                false


# Should we align to an external reference structure? If yes, give file name
#align_external_file            reference.xyz

# Reference frame for alignment (using Kabsch algorithm)
# default is "0"
ref_frame_num                   110


# Desired distance masurement unit for output
# 0: RMSD (default)
# 1: dRMSD
# 2: Hold and Sander Score

dist_unit                       0

# if Holm and Sander Score is chosen, pick value for r_c
# (contact cutoff distance)
# default is "20", as in original publication

holm_sand_r0                    5


####################################
#                                  #
#       ENTROPY-CALC OPTIONS   	   #
#                                  #
####################################

# Should alignment (Kabsch algorithm, minimizes RMSD) be performed
# prior to calculations? (options: false / true; true is default)
# entropy_ref_frame_num gives reference frame for alignment (default is 0)
entropy_alignment                 true
entropy_ref_frame_num             0

# Specify first frame to be used in entropy calculations
# default is 0
entropy_start_frame_num           0
# Specify offset value (only every n'th frame will be used in calculations)
entropy_offset                    1

# Temperature needed for Entropy etc. calculations in K
entropy_temp                      300.00

# Should the removal of degrees of freedom for rotation / translation be attempted?
entropy_remove_dof                true

# Use internal coordinates instead of cartesian coordinates?
# Use the CAST task to display the internal z-mat and then enter desired atom-indexes of bondlengths (bnd), angles (ang) and dihedral angles (dih).
# "none" also possible
entropy_use_internal              false
entropy_internal_bnd              none
entropy_internal_ang              none
entropy_internal_dih              4-23

# Should only specific atoms be used for entropy calculations?
# (only use with cartesian coordinates)
entropy_trunc_atoms_bool          false
entropy_trunc_atoms_num           3,4

# Specify method used in entropy-calculations:
# 1 : Quasi-Harmonic-Approx., configurational entropy, according to Karplus et. al. (DOI 10.1021/ma50003a019)
# 2 : Quasi-Harmonic-Approx., conformational entropy, according to Knapp et. al. without corrections (Genome Inform. 2007;18:192-205.)
# 3 : Quasi-Harmonic-Approx., conformational entropy, according to Knapp et. al. with corrections (Genome Inform. 2007;18:192-205.)
# 4 : Nearest-Neighbor Nonparametric Method, configurational entropy, according to Hnizdo et. al. (DOI: 10.1002/jcc.20589)
# 5 : Nearest-Neighbor Nonparametric Method - Sum of Marginal Entropies, configurational entropy, according to Hnizdo et. al. (DOI: 10.1002/jcc.20589)
# 6 : Quasi-Harmonic-Approx., conformational entropy, according to Schlitter (use cartesians only)
# 0 : All of the above
entropy_method                    0
# if entropy_method = 3 || 4 || 5 : specify value for k in kNN-Algorithm (default is 4)
entropy_method_knn_k              4


####################################
#                                  #
#     	PCAgen OPTIONS             #
#                                  #
####################################

# Should alignment (Kabsch algorithm, minimizes RMSD) be performed
# prior to PCA-Analysis? (options: false / true; true is default)
# pca_ref_frame_num gives reference frame for alignment (default is 0)
pca_alignment                 true
pca_ref_frame_num             0

# Specify first frame to be used in PCA-Analysis
# default is 0
pca_start_frame_num           0

# Specify offset value (only every n'th frame will be used in calculations)
#pca_offset                    1

# Should PCA-Mode-Coordinates and Eigenvalues of the covariance-matrix be written to file?
# If false, we are expecting to read Eigenvectors and PCA-Modes from a previously CAST-generated file.
pca_read_vectors              false
pca_read_modes                false

# Use internal coordinates instead of cartesian coordinates? If yes, should they converted to metric coordinate space?
# Use the CAST task to display the internal z-mat and then enter desired atom-indexes of bondlengths (bnd), angles (ang) and dihedral angles (dih).
# "none" also possible. Atom indices start at 0.
pca_use_internal              true
pca_internal_dih              5-20

# Should only specific atoms be used for PCA-Analysis?
pca_trunc_atoms_bool             true
pca_trunc_atoms_num              5-50
pca_ignore_hydrogen              false

# Print probability density of generated PCA modes?
pca_print_probability_density    true
# If true, specify the number of bins or a bin-width for histogramming the data
pca_histogram_width              0
pca_histogram_number_of_bins     42
pca_dimensions_for_histogramming 1,2

# Do you want to read in two trajectories and compare them?
pca_two_trajectories             true
# Then give here the name of the second trajectory!
pca_second_traj                  new_19_11.arc


####################################
#                                  #
#     	PCAproc OPTIONS            #
#                                  #
####################################

# Desired range of coordinates as principal components to be written.
# Specify as such: 5.0,7.0,9.0 (this means: dim1, dim2, dim3 etc....)
proc_desired_start      -5.0
proc_desired_stop       5.0