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Methods of Ex Situ and In Situ Investigations of Structural Transformations: The Case of Crystallization of Metallic Glasses
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Martini on the Rocks: Can a Coarse-Grained Force Field Model Crystals?
A Najla Hosseini1, David van der Spoel1
1Department of Cell and Molecular Biology, Uppsala University, Box 596, SE-75124 Uppsala, Sweden.
The Journal of Physical Chemistry Letters
|January 23, 2024
Summary
The Martini 3 force field inaccurately simulates amyloid peptides and organic crystals, causing structural instability and low melting points. A softer potential may improve crystal simulations.
Area of Science:
- Computational chemistry
- Molecular modeling
- Biophysics
Background:
- Coarse-grained models simplify molecular systems for large-scale simulations.
- These models are increasingly used for biomolecular system simulations.
Purpose of the Study:
- To critically evaluate the stability of amyloid peptides and organic crystals using the Martini 3 coarse-grained force field.
- To identify limitations of the Martini 3 model for simulating crystalline structures.
Main Methods:
- Simulations of amyloid peptide and organic crystal stability.
- Analysis of radial distribution functions to assess structural changes.
- Evaluation of melting points for organic compounds.
Main Results:
- Martini 3 simulations showed drastic shape changes in crystals.
- Increased distance between backbone beads in β-sheets led to crystal disruption.
- Calculated melting points for organic compounds were significantly underestimated.
Conclusions:
- Martini 3 force field lacks specific interactions for accurate peptide and organic crystal simulations without restraints.
- The 12-6 potential may contribute to inaccuracies; a softer potential could enhance crystal simulations.
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