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lorenzo-rovigatti / oxDNA

A new version of the code to simulate the oxDNA/oxRNA models, now equipped with Python bindings
https://dna.physics.ox.ac.uk/
GNU General Public License v3.0
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[DOCUMENTATION] Sequence Dependence of Cross-Stacking #108

Open alec-cook opened 1 week ago

alec-cook commented 1 week ago

Hello,

The oxDNA2_sequence_dependent_parameters.txt file provides modifiers for the stacking interaction between each pair of nucleotides. As I understand the notation, the parameter STCK_G_C modifies stacking in the dinucleotide 3'-GC-5', while STCK_C_G modifies 3'-CG-5'. I am assuming that these parameters refer specifically to the stacking between bonded neighbors; the difference between GC and CG is not well defined in the cross-stacking case, where the pair of nucleotides straddles two antiparallel strands.

How, if at all, is sequence dependence considered for cross-stacking interactions? Is the orientation of the nucleotides considered at all (e.g. is the cross-stacking between two bases that mutually face one another in the 5' direction different than the interaction between the same two bases facing one another in the 3' direction)?

Is coaxial stacking sequence-dependent in the same way as stacking between bonded neighbors?

The interaction DNA2ModInteraction, provided in /contrib/randisi, allows for a mod_stacking_multiplier to be defined. Does this multiplier affect all stacking interactions (bonded, coaxial, cross), or just the stacking between bonded neighbors?

Thank you, Alec

lorenzo-rovigatti commented 6 days ago

Hey there,

the cross- and coaxial-stacking interactions are both sequence-independent. About DNA2ModInteraction: the person who coded it left academia a few years back, I have no idea what it does.