How simple can you go? An off-the-shelf transformer approach to molecular dynamics
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arXiv
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| Format: | Preprint |
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2025
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| author | Eissler, Max Korjakow, Tim Ganscha, Stefan Unke, Oliver T. Müller, Klaus-Robert Gugler, Stefan |
| author_facet | Eissler, Max Korjakow, Tim Ganscha, Stefan Unke, Oliver T. Müller, Klaus-Robert Gugler, Stefan |
| contents | Most current neural networks for molecular dynamics (MD) include physical inductive biases, resulting in specialized and complex architectures. This is in contrast to most other machine learning domains, where specialist approaches are increasingly replaced by general-purpose architectures trained on vast datasets. In line with this trend, several recent studies have questioned the necessity of architectural features commonly found in MD models, such as built-in rotational equivariance or energy conservation. In this work, we contribute to the ongoing discussion by evaluating the performance of an MD model with as few specialized architectural features as possible. We present a recipe for MD using an Edge Transformer, an ``off-the-shelf'' transformer architecture that has been minimally modified for the MD domain, termed MD-ET. Our model implements neither built-in equivariance nor energy conservation. We use a simple supervised pre-training scheme on $\sim$30 million molecular structures from the QCML database. Using this ``off-the-shelf'' approach, we show state-of-the-art results on several benchmarks after fine-tuning for a small number of steps. Additionally, we examine the effects of being only approximately equivariant and energy conserving for MD simulations, proposing a novel method for distinguishing the errors resulting from non-equivariance from other sources of inaccuracies like numerical rounding errors. While our model exhibits runaway energy increases on larger structures, we show approximately energy-conserving NVE simulations for a range of small structures. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2503_01431 |
| institution | arXiv |
| publishDate | 2025 |
| record_format | arxiv |
| spellingShingle | How simple can you go? An off-the-shelf transformer approach to molecular dynamics Eissler, Max Korjakow, Tim Ganscha, Stefan Unke, Oliver T. Müller, Klaus-Robert Gugler, Stefan Machine Learning Most current neural networks for molecular dynamics (MD) include physical inductive biases, resulting in specialized and complex architectures. This is in contrast to most other machine learning domains, where specialist approaches are increasingly replaced by general-purpose architectures trained on vast datasets. In line with this trend, several recent studies have questioned the necessity of architectural features commonly found in MD models, such as built-in rotational equivariance or energy conservation. In this work, we contribute to the ongoing discussion by evaluating the performance of an MD model with as few specialized architectural features as possible. We present a recipe for MD using an Edge Transformer, an ``off-the-shelf'' transformer architecture that has been minimally modified for the MD domain, termed MD-ET. Our model implements neither built-in equivariance nor energy conservation. We use a simple supervised pre-training scheme on $\sim$30 million molecular structures from the QCML database. Using this ``off-the-shelf'' approach, we show state-of-the-art results on several benchmarks after fine-tuning for a small number of steps. Additionally, we examine the effects of being only approximately equivariant and energy conserving for MD simulations, proposing a novel method for distinguishing the errors resulting from non-equivariance from other sources of inaccuracies like numerical rounding errors. While our model exhibits runaway energy increases on larger structures, we show approximately energy-conserving NVE simulations for a range of small structures. |
| title | How simple can you go? An off-the-shelf transformer approach to molecular dynamics |
| topic | Machine Learning |
| url | https://arxiv.org/abs/2503.01431 |