posted on 2024-02-05, 18:38authored byManuel Palma Banos, Alexander V. Popov, Rigoberto Hernandez
We address the challenge of representativity and dynamical
consistency
when unbonded fine-grained particles are collected together into coarse-grained
particles. We implement a hybrid procedure for identifying and tracking
the underlying fine-grained particlese.g., atoms or moleculesby
exchanging them between the coarse-grained particles periodically
at a characteristic time. The exchange involves a back-mapping of
the coarse-grained particles into fine-grained particles and a subsequent
reassignment to coarse-grained particles conserving total mass and
momentum. We find that an appropriate choice of the characteristic
exchange time can lead to the correct effective diffusion rate of
the fine-grained particles when simulated in hybrid coarse-grained
dynamics. In the compressed (supercritical) fluid regime, without
the exchange term, fine-grained particles remain associated with a
given coarse-grained particle, leading to substantially lower diffusion
rates than seen in all-atom molecular dynamics of the fine-grained
particles. Thus, this work confirms the need for addressing the representativity
of fine-grained particles within coarse-grained particles and offers
a simple exchange mechanism so as to retain dynamical consistency
between the fine- and coarse-grained scales.