Academic Journal
Martini on the Rocks: Can a Coarse-Grained Force Field Model Crystals?
| العنوان: | Martini on the Rocks: Can a Coarse-Grained Force Field Model Crystals? |
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| المؤلفون: | A. Najla Hosseini, David van der Spoel |
| سنة النشر: | 2024 |
| مصطلحات موضوعية: | Biophysics, Neuroscience, Biotechnology, Computational Biology, Chemical Sciences not elsewhere classified, Physical Sciences not elsewhere classified, Information Systems not elsewhere classified, ∼ 1 å, specific interactions needed, numerous scientific disciplines, including drug discovery, grained force field, accurately simulate peptides, martini force field, martini 3 lacks, martini 3 coarse, structural biology, sheets increases, scale systems, problems may, organic compounds, molecular systems, melting points, important tool, evaluated using, critical evaluation, computational chemistry, biomolecular systems, backbone beads, amyloid peptide |
| الوصف: | Computational chemistry is an important tool in numerous scientific disciplines, including drug discovery and structural biology. Coarse-grained models offer simple representations of molecular systems that enable simulations of large-scale systems. Because there has been an increase in the adoption of such models for simulations of biomolecular systems, critical evaluation is warranted. Here, the stability of the amyloid peptide and organic crystals is evaluated using the Martini 3 coarse-grained force field. The crystals change shape drastically during the simulations. Radial distribution functions show that the distance between backbone beads in β-sheets increases by ∼1 Å, breaking the crystals. The melting points of organic compounds are much too low in the Martini force field. This suggests that Martini 3 lacks the specific interactions needed to accurately simulate peptides or organic crystals without imposing artificial restraints. The problems may be exacerbated by the use of the 12-6 potential, suggesting that a softer potential could improve this model for crystal simulations. |
| نوع الوثيقة: | article in journal/newspaper |
| اللغة: | unknown |
| Relation: | https://figshare.com/articles/journal_contribution/Martini_on_the_Rocks_Can_a_Coarse-Grained_Force_Field_Model_Crystals_/25049906 |
| DOI: | 10.1021/acs.jpclett.4c00012.s002 |
| الاتاحة: | https://doi.org/10.1021/acs.jpclett.4c00012.s002 https://figshare.com/articles/journal_contribution/Martini_on_the_Rocks_Can_a_Coarse-Grained_Force_Field_Model_Crystals_/25049906 |
| Rights: | CC BY-NC 4.0 |
| رقم الانضمام: | edsbas.B4C7F9B0 |
| قاعدة البيانات: | BASE |
| DOI: | 10.1021/acs.jpclett.4c00012.s002 |
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