Hello everyone,
Recently, I have solved a minimage distance issue while using a smaller 10$B"r(B box size with 2 RNA helices inside that. So, I have been running the simulations with a bigger box size of 15$B"r(B, but it seems like that while giving the command line in tleap, whether you use the $B!H(Biso$B!I(B command or not, the box expansion size is almost near about 70% for my case. So, has anyone faced this issue, like how to create a full $B!H(Biso$B!I(B truncated octahedron box to be sure of the fact that in all 3 directions the distance is big enough to make sure that the RNA helix from the main cell does not interact with its own image from the next image cell?
Thank you,
Subhajyoti Mandal,
Graduate Student,
David Mathews Lab, URMC
University of Rochester
601 Elmwood Avenue,
Rochester. NY 14642
Pronouns: he/him/his
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Received on Sat Jul 18 2026 - 13:00:03 PDT
