Chris Stubberup

Hi admins I used the script: data_output_1 = { print_every = 10000 name = hb_energy.dat col_1 = { type = step } col_2 = { type = hb_energy } } to generate the HB energy of my Hairpin structure. I am a bit confused about what the unit of the energy is and how much each base pair is expected to account for. From the example given with hairpin 3.5 accounts for 4-5 bonded nucleotides. The hydrogen binding energy is given from the distance between the interaction sites right so how was the 3.5 clarified...

Hi Lorenzo Thanks for the quick response! That would be amazing! Essentially i am trying to simulate the origami in an electric field, which would be F=qE on the O- charge in the backbone, to see if the structure would colapse... Best, Chris

Hi creators I am trying to simulate an origami structure, with a short repulsion acting on the backbone at intervals. I figured i could i could run a simulation with the repulsion for 1ns, and take the last configuration and put it into a new simulation without the field and so on. My problem is however, i am unsure of how i can make the force act only on the backbone. Thanks for your great work much appreciated. Best regards Chris