# SIMULATION PARAMETERS FILE ## ---- General simulation parameters ---------- SIMMETHOD SimulatedAnnealing #"Genetic" or "SimulatedAnnealing" for simulated annealing (default) or "ReplicaExchange" for replica exchange STEPS 50 #default 100; how many simulation steps to perform? ANNTEMP 1 #from range X to Y REHEAT false 1 MAXROT 15 #default is 5 MAXTRANS 5 5 5 #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 0 0 #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) ### ---- Mutation frequencies ----------- ROTATION_FREQ 0.4 #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 0.3 #from range 0 to 1, default is 0.25, sum of FREQ params must be equal to 1 EXCHANGE_FREQ 0.3 #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 1.4 #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 ### ----- 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