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Sigmoid Accelerated...
Sigmoid Accelerated Molecular Dynamics : An Efficient Enhanced Sampling Method for Biosystems
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- Zhao, Yihao (författare)
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China, Zhejiang
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- Zhang, Jintu (författare)
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China, Zhejiang; CarbonSilicon AI Technology Company, Ltd., Hangzhou 310018, Zhejiang, China, Zhejiang
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- Zhang, Haotian (författare)
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China, Zhejiang; CarbonSilicon AI Technology Company, Ltd., Hangzhou 310018, Zhejiang, China, Zhejiang
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- Gu, Shukai (författare)
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China, Zhejiang
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- Deng, Yafeng (författare)
- CarbonSilicon AI Technology Company, Ltd., Hangzhou 310018, Zhejiang, China, Zhejiang
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- Tu, Yaoquan (författare)
- KTH,Teoretisk kemi och biologi
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- Hou, Tingjun (författare)
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China, Zhejiang
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- Kang, Yu (författare)
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China, Zhejiang
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College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China, Zhejiang College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China, Zhejiang; CarbonSilicon AI Technology Company, Ltd, Hangzhou 310018, Zhejiang, China, Zhejiang (creator_code:org_t)
- 2023-01-26
- 2023
- Engelska.
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Ingår i: The Journal of Physical Chemistry Letters. - : American Chemical Society (ACS). - 1948-7185. ; 14:4, s. 1103-1112
- Relaterad länk:
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https://urn.kb.se/re...
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https://doi.org/10.1...
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Abstract
Ämnesord
Stäng
- Gaussian accelerated molecular dynamics (GaMD) is recognized as a popular enhanced sampling method for tackling long-standing challenges in biomolecular simulations. Inspired by GaMD, Sigmoid accelerated molecular dynamics (SaMD) is proposed in this work by adding a Sigmoid boost potential to improve the balance between the highest acceleration and accurate reweighting. Compared with GaMD, SaMD extends the accessible time scale and improves the computational efficiency as tested in three tasks. In the alanine dipeptide task, SaMD can produce the free energy landscape with better accuracy and efficiency. In the chignolin folding task, the estimated Gibbs free energy difference can converge to the experimental value ∼30% faster. In the protein-ligand binding task, the bound conformations are closer to the crystal structure with a minimal ligand root-mean-square deviation of 1.7 Å. The binding of the ligand XK263 to the HIV protease is reproduced by SaMD in ∼60% less simulation time.
Ämnesord
- NATURVETENSKAP -- Kemi -- Fysikalisk kemi (hsv//swe)
- NATURAL SCIENCES -- Chemical Sciences -- Physical Chemistry (hsv//eng)
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