#   SIMULATION PARAMETERS FILE


## ----   General simulation parameters   ----------

SIMMETHOD SimulatedAnnealing #"Genetic" or "SimulatedAnnealing" for simulated annealing (default) or "ReplicaExchange" for replica exchange
STEPS   3                  #default 100; how many simulation steps to perform?
ANNTEMP 1                  #from range X to Y
REHEAT false 1
#REPLICAEXCHANGE_FREQ 2      #each X steps replicas will be exchanged; by default every 10% of simulation steps
#REPLICATEMPERATURES 200 100 50 0 # 400 375 350 325 300 275 250 225 200 175 150 125 100 #list of temperatures for all replicas
MAXROT 15                     #default is 5
MAXTRANS    15 15 15            #default is [5, 5, 5]

## ---    Scoring function parameters      ----------
OUTBOX 1 1                   #default 1 1; can be in range from 0 to 10 (float numbers)
MAP_FREESPACE  1 0           #default 1 1; can be in range from 0 to 10 (float numbers); also used for SAXS shapes
CLASHES   1 0                #default 1 1; can be in range from 0 to 10 (float numbers)
#CLASHES_ALLATOMS   1 1       #default 1 1; can be in range from 0 to 10 (float numbers)
RESTRAINTS  1 1              #default 1 1; can be in range from 0 to 10 (float numbers)
DENSITY     0 0               #default 1 1; can be in range from 0 to 10 (float numbers)
SYMMETRY    1 1

### ----  Mutation frequencies -----------
ROTATION_FREQ 0.5           #from range 0 to 1, default is 0.25, sum of FREQ params must be equal to 1
ROTATION_COV_FREQ 0.0       #from range 0 to 1, default is 0.25, sum of FREQ params must be equal to 1
TRANSLATION_FREQ 0.5        #from range 0 to 1, default is 0.25, sum of FREQ params must be equal to 1
EXCHANGE_FREQ 0.0           #from range 0 to 1, default is 0.25, sum of FREQ params must be equal to 1
SIMUL_DD_FREQ 0.0           #from range 0 to 1, default is 0.25, sum of FREQ params must be equal to 1
TRANSLATION_ALL_FREQ 0.0    #from range 0 to 1, default is 0.25, sum of FREQ params must be equal to 1; mutation were all components are translated together
ROTATION_ALL_FREQ 0.0       #from range 0 to 1, default is 0.25, sum of FREQ params must be equal to 1; mutation were all components are translated together


## -----  Input data descriptors   --------
THRESHOLD 1.6                #float value existing in map file, default is 0
#KVOL 0.3
SIMBOX 1.2                   #default simulation box diameter
GRIDRADIUS  2.0              #default is 1.0
GRIDTYPE    cubic                #cubic or diamond
COMPONENT_REPRESENTATION ca  #CA - only calfas/c4' (default); cacb - coarse grain, 3p - 3points, fa - full atom
SAXSRADIUS 2                #dummy atom radius for ab initio SAXS reconstruction


### ----- Simulation process control -------
SCALEPARAMS on               #on/off
PARAMSCALINGRANGES 0 25 50   #default 0 25 50; at what point of simulation should parameter scaling ranges kick in; % zakresu symulacji (postep)
PARAMSCALINGR1 50 100        #default 50 100 in %
PARAMSCALINGR2 25 50         #default 25 50 in %
PARAMSCALINGR3 0 25          #default 0 25 in %


## ------ Output parameters ---------

WRITE_N_ITER 1              #default 0, minimum 1 max=STRUCT_NR
#WRITE_EACHBETTER True
#OUT_STEPS   10 15           #default one struct with best score; which steps in output data?
#STRUCT_NR  14              #default 0.1*SIMUL_NR; number ot out structure with best scores


#COMPONENTS MOVEMENTS INFORMATION


#MOVE_STATE  A   fixed
#MOVE_STATE  Z   fixed
#MOVE_STATE  X   fixed
#MOVE_STATE  X_protein   fixed
#MOVE_STATE  D   movable 1 1 1 3 3 3 2 2 2 4 4 4 5 30 #max_rot_angle; axis *3; maxtrans, sum_rots, sum_trans, around_line rot_single, rot_sum
#MOVE_STATE  A   movable 2 2 2 2 2 2 3 3 3 3 3 3 5 90 #max_rot_angle; axis *3; maxtrans
#MOVE_STATE  Z   movable 3 3 3 1 1 1 4 4 4 2 2 2 5 90 #max_rot_angle; axis *3; maxtrans
#START_ORIENTATION true     #True if user sets start conformation, False if not!!


#define components that are mutated together; eg. A [Z,D] if A is rotated/translated then Z and D will be also rotated/translated
#COVALENT_BONDS A ['Z','D'] [10,'CA'] [11,'CA']   #to indicate which components are covalently bonded
#COVALENT_BONDS A ['D'] [5,'CA'] [7,'CA']
#COVALENT_BONDS D ['A']    #to indicate which components are covalently bonded
#COVALENT_BONDS Z ['A']  [14,'CA'] [15,'CA']  #to indicate which components are covalently bonded

#COVALENT_BONDS A [B]    #to indicate which components are covalently bonded
#COVALENT_BONDS B [A,C]  #to indicate which components are covalently bonded
#COVALENT_BONDS C [B]    #to indicate which components are covalently bonded
#COVALENT_BONDS D [E,F]  #to indicate which components are covalently bonded
#COVALENT_BONDS E [D]    #to indicate which components are covalently bonded
#COVALENT_BONDS F [D]    #to indicate which components are covalently bonded



#   EXAMPLES

#use density map equal to 10 complex volumes
#KVOL 10

#use density map with density values >= threshold equal to 1.5
#THRESHOLD 1.5

#perform only 5 simulation steps
#STEPS   5

#perform default number of steps
#STEPS   X

#“give me the structure with best score”

#OUT_STEPS   FIRST   LAST 
#STRUCT_NR   1 

#“give me structures with 100 best scores”

#OUT_STEPS   FIRST   LAST 
#STRUCT_NR   100

#“give me all structures from the part of trajectory, steps: 13548-13570”

#OUT_STEPS   13548   13570 
#STRUCT_NR   22

#“give me the structure with 7th best score among all structures
#from the part of trajectory, steps: 13548-13570”

#OUT_STEPS   13548   13570
#STRUCT_NR   7
