Valency-bounding correction potential for coarse-grained molecular dynamics simulations
Abstract
Many systems in soft and living matter bind through a limited number of bonds per particle: proteins associate via discrete surface patches, nucleic acids form one-to-one contacts, and the phase behaviour of multivalent biomolecules is governed by the number of binding sites they carry. In simulations, valency limits are typically enforced with patchy particles, whose anisotropic potentials require integration of rotational degrees of freedom and combine hard cores with narrow patches, which forces small timesteps and commits the model to a fixed binding-site geometry that is often unknown, flexible or mobile. We introduce the valency-bounding correction (VBC), a many-body modification of generic short-range pairwise potentials that smoothly suppresses attraction once the neighbour count of either interacting particle exceeds a prescribed valency. The correction carries no angular degrees of freedom, applies on top of soft repulsive cores and evaluates in two passes over the neighbour list at the cost of a standard pairwise potential. The VBC drives the coordination number to the prescribed valency with low error, while its cluster statistics depart from Wertheim and Flory-Stockmayer predictions through unrestricted ring formation. A tuned variant exchanges bonded partners through ordinary molecular dynamics, reducing bond lifetimes at high saturation by an order of magnitude. On GPUs the cost of the correction is nearly independent of valency, reaching an almost tenfold advantage over a patchy-particle reference. We illustrate large-scale applications by reproducing the reentrant aggregation of repeat-expanded RNA, and show that the VBC also remedies the Fisher-Ruelle thermodynamic instability of soft-core potentials with attraction. The VBC is available as an open-source GPU plugin for HOOMD-blue.
Related
- Thermo-elastic properties of hydrated epoxy-graphene nanocomposites from ensemble-based molecular dynamics simulations
- Predicting energy and structural response to force correction in molecular dynamics
- Molecular dynamics simulations of DMSO-MeOH liquid mixtures. Effects of force fields on mixing properties
- Full molecular dynamics simulations of a single trapped ion in a neutral bath
- Strain-Induced BCC-to-FCC Transformation in Tungsten Uncovered by Molecular Dynamics Simulations with Machine Learning Potentials
BibTeX
@misc{dmitriev2026valencybounding,
title = {{Valency-bounding correction potential for coarse-grained molecular dynamics simulations}},
author = {Vladimir Dmitriev and Ankit Gupta and Anton Goloborodko},
howpublished = {arXiv},
year = {2026},
month = sep,
doi = {10.48550/arxiv.2609.07842},
eprint = {2609.07842},
archivePrefix = {arXiv},
url = {https://arxiv.org/abs/2609.07842},
note = {CC BY 4.0},
}
RIS
TY - UNPB
TI - Valency-bounding correction potential for coarse-grained molecular dynamics simulations
AU - Vladimir Dmitriev
AU - Ankit Gupta
AU - Anton Goloborodko
PY - 2026
DA - 2026/09/07
PB - arXiv
DO - 10.48550/arxiv.2609.07842
UR - https://arxiv.org/abs/2609.07842
AB - Many systems in soft and living matter bind through a limited number of bonds per particle: proteins associate via discrete surface patches, nucleic acids form one-to-one contacts, and the phase behaviour of multivalent biomolecules is governed by the number of binding sites they carry. In simulations, valency limits are typically enforced with patchy particles, whose anisotropic potentials require integration of rotational degrees of freedom and combine hard cores with narrow patches, which forces small timesteps and commits the model to a fixed binding-site geometry that is often unknown, flexible or mobile. We introduce the valency-bounding correction (VBC), a many-body modification of generic short-range pairwise potentials that smoothly suppresses attraction once the neighbour count of either interacting particle exceeds a prescribed valency. The correction carries no angular degrees of freedom, applies on top of soft repulsive cores and evaluates in two passes over the neighbour list at the cost of a standard pairwise potential. The VBC drives the coordination number to the prescribed valency with low error, while its cluster statistics depart from Wertheim and Flory-Stockmayer predictions through unrestricted ring formation. A tuned variant exchanges bonded partners through ordinary molecular dynamics, reducing bond lifetimes at high saturation by an order of magnitude. On GPUs the cost of the correction is nearly independent of valency, reaching an almost tenfold advantage over a patchy-particle reference. We illustrate large-scale applications by reproducing the reentrant aggregation of repeat-expanded RNA, and show that the VBC also remedies the Fisher-Ruelle thermodynamic instability of soft-core potentials with attraction. The VBC is available as an open-source GPU plugin for HOOMD-blue.
ER -