ArticleJournal of chemical theory and computation2025
GridFF: Efficient Simulation of Organic Molecules on Rigid Substrates.
Article in Journal of chemical theory and computation, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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4 authors.
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Abstract
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 100-1000× 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
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