Currently, the oxDNA export algorithm for loopouts puts the nucleotides along a straight line in between the two domains it joins. If there are many nucleotides and the domains are close together, then this linear interpolation places the nucleotides extremely close to each other.
scadnano design:
oxDNA export (note the loopout of length 32 in the lower left):
which explodes the molecular dynamics simulation due to the very large forces they exert on each other in such close proximity.
Currently, the oxDNA export algorithm for loopouts puts the nucleotides along a straight line in between the two domains it joins. If there are many nucleotides and the domains are close together, then this linear interpolation places the nucleotides extremely close to each other.
scadnano design:
oxDNA export (note the loopout of length 32 in the lower left):
which explodes the molecular dynamics simulation due to the very large forces they exert on each other in such close proximity.