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| Auteurs principaux: | , , , |
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| Format: | Preprint |
| Publié: |
2025
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| Sujets: | |
| Accès en ligne: | https://arxiv.org/abs/2508.15522 |
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| _version_ | 1866915455610912768 |
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| author | Mal, Indranil Kočí, Milan Nicolini, Paolo Hapala, Prokop |
| author_facet | Mal, Indranil Kočí, Milan Nicolini, Paolo Hapala, Prokop |
| contents | We present GridFF, an efficient method for simulating molecules on rigid substrates, derived from techniques used in protein-ligand docking in biochemistry. By projecting molecule-substrate interactions onto precomputed spatial grids with tricubic B-spline interpolation, GridFF reduces the computational cost by orders of magnitude compared to traditional pairwise atomistic models, without compromising the accuracy of forces or trajectories. The CPU implementation of GridFF in the open-source FireCore package provides a 100-1000x speedup over all-atom simulations using LAMMPS, while the GPU implementation - running thousands of system replicas in parallel - samples millions of configurations per second, enabling an exhaustive exploration of the configuration space of small flexible molecules on surfaces within minutes. Furthermore, as demonstrated in our previous application of a similar technique to high-resolution scanning probe microscopy, GridFF can be extended beyond empirical pairwise potentials to those derived from ab initio electron densities. Altogether, this unlocks accurate high-throughput modeling of molecular self-assembly, adsorption, and scanning probe manipulation in surface science. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2508_15522 |
| institution | arXiv |
| publishDate | 2025 |
| record_format | arxiv |
| spellingShingle | GridFF: Efficient Simulation of Organic Molecules on Rigid Substrates Mal, Indranil Kočí, Milan Nicolini, Paolo Hapala, Prokop Chemical Physics We present GridFF, an efficient method for simulating molecules on rigid substrates, derived from techniques used in protein-ligand docking in biochemistry. By projecting molecule-substrate interactions onto precomputed spatial grids with tricubic B-spline interpolation, GridFF reduces the computational cost by orders of magnitude compared to traditional pairwise atomistic models, without compromising the accuracy of forces or trajectories. The CPU implementation of GridFF in the open-source FireCore package provides a 100-1000x speedup over all-atom simulations using LAMMPS, while the GPU implementation - running thousands of system replicas in parallel - samples millions of configurations per second, enabling an exhaustive exploration of the configuration space of small flexible molecules on surfaces within minutes. Furthermore, as demonstrated in our previous application of a similar technique to high-resolution scanning probe microscopy, GridFF can be extended beyond empirical pairwise potentials to those derived from ab initio electron densities. Altogether, this unlocks accurate high-throughput modeling of molecular self-assembly, adsorption, and scanning probe manipulation in surface science. |
| title | GridFF: Efficient Simulation of Organic Molecules on Rigid Substrates |
| topic | Chemical Physics |
| url | https://arxiv.org/abs/2508.15522 |