  We present a new method for calculating internal forces in DNA structures
using coarse-grained models and demonstrate its utility with the oxDNA model.
The instantaneous forces on individual nucleotides are explored and related to
model potentials, and using our framework, internal forces are calculated for
two simple DNA systems and for a recently-published nanoscopic force clamp. Our
results highlight some pitfalls associated with conventional methods for
estimating internal forces, which are based on elastic polymer models, and
emphasise the importance of carefully considering secondary structure and ionic
conditions when modelling the elastic behaviour of single-stranded DNA. Beyond
its relevance to the DNA nanotechnological community, we expect our approach to
be broadly applicable to calculations of internal force in a variety of
structures -- from DNA to protein -- and across other coarse-grained simulation
models.

Soft Condensed Matter;Biological Physics