Enhancing pressure consistency and transferability of structure-based coarse-graining

• Published in: Physical chemistry chemical physics : PCCP Vol. 25; no. 3; pp. 2256 - 2264
• Main Authors: Tang, Jiahao, Kobayashi, Takayuki, Zhang, Hedong, Fukuzawa, Kenji, Itoh, Shintaro
• Format: Journal Article
• Language: English
• Published: England Royal Society of Chemistry 18.01.2023
• Subjects: Beads; Distribution functions; Dodecane; Ellipsoids; Granulation; Iterative methods; Low pressure; Molecular dynamics; Molecular structure; Radial distribution; Simulation
• DOI: 10.1039/d2cp04849c
• ISSN: 1463-9076

Coarse-graining, which models molecules with coarse-grained (CG) beads, allows molecular dynamics simulations to be applied to systems with large length and time scales while preserving the essential molecular structure. However, CG models generally have insufficient representability and transferability. A commonly used method to resolve this problem is multi-state iterative Boltzmann inversion (MS-IBI) with pressure correction, which matches both the structural properties and pressures at different thermodynamic states between CG and all-atom (AA) simulations. Nevertheless, this method is usually effective only in a narrow pressure range. In this paper, we propose a modified CG scheme to overcome this limitation. We find that the fundamental reason for this limitation is that CG beads at close distances are ellipsoids rather than isotropically compressed spheres, as described in conventional CG models. Hence, we propose a method to compensate for such differences by slightly modifying the radial distribution functions (RDFs) derived from AA simulations and using the modified RDFs as references for pressure-corrected MS-IBI. We also propose a method to determine the initial non-bonded potential using both the target RDF and pressure. Using n -dodecane as a case study, we demonstrate that the CG model developed using our scheme reproduces the RDFs and pressures over a wide range of pressure states, including three reference low-pressure states and two test high-pressure states. The proposed scheme allows for accurate CG simulations of systems in which pressure or density varies with time and/or position. A modified coarse-graining scheme, which compensates for the compression of coarse-grained beads at close distances in conventional models, enhances pressure consistency and transferability.