oxDNA2_average_sequence_parameters.txt

# file that reproduces the average sequence file for oxDNA2
#
# start from this and modify it as you want if e.g. you want to shut down hydrogen bonds,
# or change the stacking strengths, etc.

STCK_FACT_EPS = 0.180004
STCK_G_C = 1.6491556
STCK_C_G = 1.6491556
STCK_G_G = 1.6491556
STCK_C_C = 1.6491556
STCK_G_A = 1.6491556
STCK_T_C = 1.6491556
STCK_A_G = 1.6491556
STCK_C_T = 1.6491556
STCK_T_G = 1.6491556
STCK_C_A = 1.6491556
STCK_G_T = 1.6491556
STCK_A_C = 1.6491556
STCK_A_T = 1.6491556
STCK_T_A = 1.6491556
STCK_A_A = 1.6491556
STCK_T_T = 1.6491556
# notice that this is not 1.058875, which is the average of the hydrogen bonding terms, but is the value
# defined into the model.h file
HYDR_A_T = 1.0678
HYDR_T_A = 1.0678
HYDR_C_G = 1.0678
HYDR_G_C = 1.0678