MDAnalysis is an object-oriented Python library to analyze trajectories from molecular dynamics (MD) simulations in many popular formats. It can write most of these formats, too, together with atom selections suitable for visualization or native analysis tools.
MDAnalysis allows one to read particle-based trajectories (including individual coordinate frames such as biomolecules in the PDB format) and access the atomic coordinates through NumPy arrays. This provides a flexible and relatively fast framework for complex analysis tasks. In addition, powerful atom selection commands are implemented. Trajectories can also be manipulated (for instance, fit to a reference structure) and written out.
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https://www.mdanalysis.org/
MDAnalysis allows one to read particle-based trajectories (including individual coordinate frames such as biomolecules in the PDB format) and access the atomic coordinates through NumPy arrays. This provides a flexible and relatively fast framework for complex analysis tasks. In addition, powerful atom selection commands are implemented. Trajectories can also be manipulated (for instance, fit to a reference structure) and written out.
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https://www.mdanalysis.org/
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* CREST 3.0 IS AVAILABLE! *
CREST 3.0 is a major overhaul of the previous code versions. A large part of the original source code was rewritten to implement calculators, optimization, and molecular dynamics routines directly, rather than relying only on the xtb program as a subprocess.
Consequently, there are performance improvements and a significant reduction of I/O operations.
Features include:
* Major code refactoring
* New input file reader
* Energy- and gradient-based interface for calculations
* Standalone ANCOPT implementation (RF optimizer with BFGS update step in approximate normal coordinates)
* Standalone MD and metadynamics module
* Standalone implementation of geometrical constraints
* New minimum energy crossing point (MECP) algorithm (see JCTC, 2022, 18 (10), 6370-6385.)
* Integration of the tblite submodule
* Integration of a GFN0-xTB submodule (see J. Phys. Chem. Lett. 2023, 14, 19, 4440–4448)
* Integration of the TOML-F parser
* Integration of a GFN-FF submodule
* Implementation of a multi-layered multi-center ONIOM calculator (see J. Phys. Chem. B 2024, 128, 13, 3145–3156, @paw61)
* Proper unit tests for the CMake build
* MSREACT mode (@gorges97)
* Implementation of X-HCFF (@zellerf)
* Effective Hessian calculator (@GereonFeldmann)
* and more ...
📄 READ the paper:
https://pubs.aip.org/aip/jcp/article/160/11/114110/3278084/CREST-A-program-for-the-exploration-of-low-energy
💻 get the code here:
https://github.com/crest-lab/crest/releases/tag/v3.0
CREST 3.0 is a major overhaul of the previous code versions. A large part of the original source code was rewritten to implement calculators, optimization, and molecular dynamics routines directly, rather than relying only on the xtb program as a subprocess.
Consequently, there are performance improvements and a significant reduction of I/O operations.
Features include:
* Major code refactoring
* New input file reader
* Energy- and gradient-based interface for calculations
* Standalone ANCOPT implementation (RF optimizer with BFGS update step in approximate normal coordinates)
* Standalone MD and metadynamics module
* Standalone implementation of geometrical constraints
* New minimum energy crossing point (MECP) algorithm (see JCTC, 2022, 18 (10), 6370-6385.)
* Integration of the tblite submodule
* Integration of a GFN0-xTB submodule (see J. Phys. Chem. Lett. 2023, 14, 19, 4440–4448)
* Integration of the TOML-F parser
* Integration of a GFN-FF submodule
* Implementation of a multi-layered multi-center ONIOM calculator (see J. Phys. Chem. B 2024, 128, 13, 3145–3156, @paw61)
* Proper unit tests for the CMake build
* MSREACT mode (@gorges97)
* Implementation of X-HCFF (@zellerf)
* Effective Hessian calculator (@GereonFeldmann)
* and more ...
📄 READ the paper:
https://pubs.aip.org/aip/jcp/article/160/11/114110/3278084/CREST-A-program-for-the-exploration-of-low-energy
💻 get the code here:
https://github.com/crest-lab/crest/releases/tag/v3.0
AIP Publishing
CREST—A program for the exploration of low-energy molecular chemical space
Conformer–rotamer sampling tool (CREST) is an open-source program for the efficient and automated exploration of molecular chemical space. Originally developed
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We have noticed an increase in spammers and users posting unrelated, and sometimes offensive, comments and content 🚫. This group has active moderation and we try to act as fast as possible. Please be aware that users who do not comply with the rules may be banned without warning ⚠️.
Remember to write in English 📝, stay on topic 🔍, and be respectful to your colleagues 🤝.
Have fun! 🎉
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Electron videography captures moving dance between proteins and lipids
https://phys.org/news/2024-04-electron-videography-captures-proteins-lipids.html
https://phys.org/news/2024-04-electron-videography-captures-proteins-lipids.html
phys.org
Electron videography captures moving dance between proteins and lipids
In a first demonstration of "electron videography," researchers have captured a microscopic moving picture of the delicate dance between proteins and lipids found in cell membranes. The technique can ...
Researchers detect a new molecule in space https://phys.org/news/2024-04-molecule-space.html
phys.org
Researchers detect a new molecule in space
New research from the group of MIT Professor Brett McGuire has revealed the presence of a previously unknown molecule in space. The team's open-access paper, "Rotational Spectrum and First Interstellar ...