More information about the reaction criteria ( defined in mod_ReactionCriteria.f90 ).
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It is necessary to define a set of reaction criteria for :

Association rate calculations, type_reaction = assoc_rate
Docking, type_reaction = docking
Electron transfer,type_reaction = elec_transfert

By default, the object is switiched off with type_reaction = off_rc

Both association rates and a limited docking simulations can be performed at the same time, but the rules for recording the complexes are simplified

The reaction criteria input file consists of a set of definitions like :

 #keyword                              criteria for solute 1  | distance|                                 criteria for solute 2
 CNONS ATOM    540  OE2 GLU A  60      26.527  32.135  -0.455 |    60.00| ATOM    332  N   LEU D  34      28.306  33.610   1.176

They consist of a keyword of 5 letters, an non read block of X letter, the position of the reaction criteria of the solute 1, the distance criteria, a non-read block and the position of the reaction criteria of the solute 2

Warning: This is fortran code, the line should follow exactly the same formatting

If solutes are not flexible, only the position of the atoms are read from the line. Otherwise the atom number is read and stored. And then the position of the atoms, for each conformation, will be read from the pdb input file.

Docking simulations need to define a set of reaction criteria with keywords :

CSPEC for a specific reaction. The distance between the atoms defining the reaction must be less than the distance defined in order for a complex to be recorded.
CNONS for a non-specific reaction. Complexes are recorded when a certain number (or greater) of non-specific reaction criteria are met (as with specific reaction criteria, the distance between atoms defining the reaction criteria must be less than the defining distance). The number of non-specific criteria that must be met to record a complex is given by nnnons in the input file, and stored in the variable nnons_min.
ASPEC for an anti-specific reaction. Here the distance between the atoms defining the reaction must be GREATER THAN the defined distance in order for a complex to be complex to be recorded.

All theses requirements must be met for the complex to be accepted and recorded in the complex file. For example, if you define two specific reaction criteria, three non-specific reaction criteria, and set nnnons to two. The two defined specific criteria, and at least two of the non-specific criteria, must be met for a complex to be recorded.

Association rate calculations will record the number of contacts which is formed at some distance.
You specify in the GROUP RateCalculation the maximum number of contacts with the keyword nb_contact in the sda input file,
and the distance in defining the distance of the closest window ( first_window ), the number of windows ( nb_window ) and the width of the windows ( width_window ).
All theses parameters are stored as data members of mod_rate_calculation::association_rate
In this case you can still record complexes but all reaction criteria are considered as non specific ( CNONS ).
Only the complexes which satisfy both :

nnnons : the minimum number of contatcs formed
nwrec : a fixed window number, at which the number of contacts will be computed will be recorded in the complex file. The same rules for inserting complexes are applied

Additionaly some pairs of independent contacts can be defined with the dind parameter.
If 2 reaction criteria of the same solute are at a distance smaller than dind, only 1 reaction will be considered.
You can see in reaction_criteria.log, how many of the criteria are considered as independent.