How to devide the HB ENERGY into each DNA molecules

[masakikato001]

How to devide the HB ENERGY into each DNA molecules

[lorenzo-rovigatti]

Hi! First of all, unfortunately there was a typo in the documentation: base_file should have read bases_file. Sorry about that.
Having said that, hb_energy gives you the total HB energy, so you probably want to have a separate column for each strand. Something like this:

data_output_1 = {
	print_every = 10000
	name = hb_energy.dat
	col_1 = {
		type = step
	}
	col_2 = {
		type = hb_energy
		bases_file = bases_1.dat
	}
	col_3 = {
		type = hb_energy
		bases_file = bases_2.dat
	}
	col_4 = {
		type = hb_energy
		bases_file = bases_3.dat
	}
}

where bases_1.dat is

0
1
2

bases_2.dat is

3
4
5

and bases_3.dat is

6
7
8

Note that nucleotide ids are 0-indexed.

[masakikato001]

Hi, lorenzo. Thank you for your kind reply.
I confirmed that the calculation was operated properly.