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bioRxiv · 10.64898/2026.03.18.712524

OpenCafeMol with 3SPN.2 DNA model: GPU Acceleration for Long-Time Coarse-Grained Chromatin Simulations

Yamauchi, M.·Murata, Y.·Niina, T.·Takada, S.
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Abstract

There is a growing demand for molecular dynamics simulations to explore longer timescale behavior of giant protein-DNA complexes such as chromatin. To address this need, we extended OpenCafeMol, a GPU-accelerated residue-level coarse-grained molecular dynamics simulator originally developed for proteins and lipids, to support 3SPN.2 and 3SPN.2C DNA models. We also implemented a hydrogen-bond-type many-body potential to model DNA-protein interactions more accurately. To further improve computational efficiency, we introduced a localized scheme for calculating base-pairing and cross-stacking interactions. Benchmark tests show that OpenCafeMol on a single GPU achieves up to 200-fold speed-up for DNA-only systems and up to 100-fold speed-up for DNA-protein complexes compared to CPU-based simulations. To demonstrate the capability of our implementation for long-timescale biological processes, we simulated an archaeal SMC-ScpA complex undergoing DNA translocation via segment capture (a proposed mechanism for DNA loop extrusion) in the presence of a DNA-bound obstacle. We observed continuous captured-loop growth accompanied by obstacle bypass within the segment capture framework.

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Yamauchi, M., Murata, Y., Niina, T., Takada, S.. 2026-03-19. OpenCafeMol with 3SPN.2 DNA model: GPU Acceleration for Long-Time Coarse-Grained Chromatin Simulations. https://doi.org/10.64898/2026.03.18.712524

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