Activity for Chris Stubberup
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Chris Stubberup posted a comment on discussion General Discussion
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...
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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
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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
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