On behalf of the Amber development team, I am pleased to announce the release of AmberTools23. Thanks to all who contributed to this. Details and downloading instructions are here: https://ambermd.org/
This is also a good time to remind people that Amber22 (basically, the pmemd program) is now also free for non-commercial use. We encourage people using older versions of Amber to update: https://ambermd.org/GetAmber.php
This is also a good time to remind people that Amber22 (basically, the pmemd program) is now also free for non-commercial use. We encourage people using older versions of Amber to update: https://ambermd.org/GetAmber.php
ambermd.org
The Amber Molecular Dynamics Package
Amber is a package of programs for
molecular dynamics simulations of proteins and nucleic acids
molecular dynamics simulations of proteins and nucleic acids
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Benzene’s forgotten isomer takes centre stage in organic synthesis | Research | Chemistry World
https://www.chemistryworld.com/news/benzenes-forgotten-isomer-takes-centre-stage-in-organic-synthesis/4017364.article
https://www.chemistryworld.com/news/benzenes-forgotten-isomer-takes-centre-stage-in-organic-synthesis/4017364.article
Chemistry World
Benzene’s forgotten isomer takes centre stage in organic synthesis
1,2,3-cyclohexatriene proves to be an unexpected hit as a reagent in a wide range of reactions
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Elicit - AI tool to help finding literature for your research
Elicit is a research assistant using language models like GPT-3 to automate parts of researchers’ workflows. Currently, the main workflow in Elicit is Literature Review. If you ask a question, Elicit will show relevant papers and summaries of key information about those papers in an easy-to-use table.
🔗 - https://elicit.org/
Elicit is a research assistant using language models like GPT-3 to automate parts of researchers’ workflows. Currently, the main workflow in Elicit is Literature Review. If you ask a question, Elicit will show relevant papers and summaries of key information about those papers in an easy-to-use table.
🔗 - https://elicit.org/
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A nice cloud storage platform called 'infiniCloud' from Japan is recently released. New user can get 20GB free space. After applying some coupon code and clicking two links, one can get additional 25GB space (in total 45GB=20+5+10+10).
This cloud disk can be accessed on Linux/Windows/MacOS/Android/iOS via WebDav protocol. (check this page for more details https://infini-cloud.net/en/clients.html)
If you are interested, please check https://infini-cloud.net/en/index.html. After registering, you may enter the ref code 4M538 to get the 5GB bonus space.
To get additional 10GBx2, click
https://infini-cloud.net/en/modules/bonus/code=202304_10GB_jp/userid=MYUSERNAME
https://infini-cloud.net/en/modules/bonus/code=202304_10GB_en/userid=MYUSERNAME
[replace MYUSERNAME with your own username]
company info: https://infini-cloud.net/en/about.html
security measure info: https://infini-cloud.net/en/support_service_server.html
maximum speed: 200Mbps per IP address (https://infini-cloud.net/en/support_guide_general_speed.html)
underlying infrastructure: Solaris ZFS storage arrays in a RAIDZ-3 (https://infini-cloud.net/en/support_guide_general_storage.html)
inactive account: account with two-year inactivity will be deleted (https://infini-cloud.net/en/support_account_term.html)
transfer protocol: WebDAV (HTTPS)
Hope it helps! 😊
This cloud disk can be accessed on Linux/Windows/MacOS/Android/iOS via WebDav protocol. (check this page for more details https://infini-cloud.net/en/clients.html)
If you are interested, please check https://infini-cloud.net/en/index.html. After registering, you may enter the ref code 4M538 to get the 5GB bonus space.
To get additional 10GBx2, click
https://infini-cloud.net/en/modules/bonus/code=202304_10GB_jp/userid=MYUSERNAME
https://infini-cloud.net/en/modules/bonus/code=202304_10GB_en/userid=MYUSERNAME
[replace MYUSERNAME with your own username]
company info: https://infini-cloud.net/en/about.html
security measure info: https://infini-cloud.net/en/support_service_server.html
maximum speed: 200Mbps per IP address (https://infini-cloud.net/en/support_guide_general_speed.html)
underlying infrastructure: Solaris ZFS storage arrays in a RAIDZ-3 (https://infini-cloud.net/en/support_guide_general_storage.html)
inactive account: account with two-year inactivity will be deleted (https://infini-cloud.net/en/support_account_term.html)
transfer protocol: WebDAV (HTTPS)
Hope it helps! 😊
InfiniCLOUD
Apps|InfiniCLOUD | All-In-One Cloud Storage | Get 20GB Free
Large capacity online storage. Fast and comfortable use of Japanese servers. Create an account and get 10 GB free
❤3👍1
FreeDTS
FreeDTS is software to perform computational research on biomembranes at messocpic length-scale.
https://github.com/weria-pezeshkian/FreeDTS
FreeDTS is software to perform computational research on biomembranes at messocpic length-scale.
https://github.com/weria-pezeshkian/FreeDTS
GitHub
GitHub - weria-pezeshkian/FreeDTS: a package to simulate fluid surfaces and biomembranes
a package to simulate fluid surfaces and biomembranes - weria-pezeshkian/FreeDTS
❤1👍1
Elk version 8.8.26 has just been released
———————————————————-
This version features molecular dynamics using atomic trajectories
determined from the Hellman-Feynman + IBS forces. See the examples in
the elk/examples/molecular-dynamics directory for details. This
technique can also be used as a simple structural prediction method
using simulated annealing. Furthermore, the molecular dynamics forces
can be subsequently used in a TDDFT Ehrenfest calculation, although this
should be considered an experimental feature.
The new version is faster and more stable for most tasks.
Also included are examples of the electron-phonon coupled Bogoliubov
equations as described in Phys. Rev. B 105, 174509 (2022). See the
elk/examples/Bogoliubov directory.
https://sourceforge.net/projects/elk/
———————————————————-
This version features molecular dynamics using atomic trajectories
determined from the Hellman-Feynman + IBS forces. See the examples in
the elk/examples/molecular-dynamics directory for details. This
technique can also be used as a simple structural prediction method
using simulated annealing. Furthermore, the molecular dynamics forces
can be subsequently used in a TDDFT Ehrenfest calculation, although this
should be considered an experimental feature.
The new version is faster and more stable for most tasks.
Also included are examples of the electron-phonon coupled Bogoliubov
equations as described in Phys. Rev. B 105, 174509 (2022). See the
elk/examples/Bogoliubov directory.
https://sourceforge.net/projects/elk/
SourceForge
Elk
Download Elk for free. An all-electron full-potential linearised augmented-planewave (FP-LAPW) code. Designed to be as developer friendly as possible so that new developments in the field of density functional theory (DFT) can be added quickly and reliably.
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Scientists Discover a New Class of “Molecular Motors”
https://scitechdaily.com/scientists-discover-a-new-class-of-molecular-motors/
https://scitechdaily.com/scientists-discover-a-new-class-of-molecular-motors/
SciTechDaily
Scientists Discover a New Class of “Molecular Motors”
Cells possess a remarkable ability to organize their interiors using minuscule protein machines known as molecular motors, which generate directed motion. Most molecular motors rely on a common form of chemical energy, ATP, to function. Recently, a team of…
Theoretical Physicists Discover Why Optical Cavities Slow Down Chemical Reactions
https://scitechdaily.com/theoretical-physicists-discover-why-optical-cavities-slow-down-chemical-reactions/
https://scitechdaily.com/theoretical-physicists-discover-why-optical-cavities-slow-down-chemical-reactions/
SciTechDaily
Theoretical Physicists Discover Why Optical Cavities Slow Down Chemical Reactions
Scientists have discovered why chemical reactions are slowed down in mirrored cavities, where molecules interact with light. The team used Quantum-Electrodynamical Density-Functional Theory to find that the conditions inside the optical cavity affected the…
Beyond the Spectrum: Machine Learning Unlocks Predictive Power in Organic Chemistry Research
https://scitechdaily.com/beyond-the-spectrum-machine-learning-unlocks-predictive-power-in-organic-chemistry-research/
https://scitechdaily.com/beyond-the-spectrum-machine-learning-unlocks-predictive-power-in-organic-chemistry-research/
SciTechDaily
Beyond the Spectrum: Machine Learning Unlocks Predictive Power in Organic Chemistry Research
Scientists have developed a machine-learning algorithm that predicts electron energy levels in organic molecules. This breakthrough, trained on a database of over 22,000 molecules, could accelerate the design of functional molecules like pharmaceuticals.…
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Chemfp 4.1 was released
Chemfp - Fast cheminformatics fingerprint search, anywhere you use Python
📄 Chemfp is an analytics platform for cheminformatics fingerprints. It contains command-line tools and an extensive Python library for fingerprint generation, high-performance similarity search, diversity selection, and exploratory research.
# Why chemfp?
* Do you want single-threaded search of 1M 1024-bit fingerprints in under 10 milliseconds?
* Do you want to make a sparse similarity matrix from 1M 2048-bit fingerprints in less than 30 minutes on a four core machine?
* Do you want to include fingerprint similarity results in your Python web application?
... with fast reload times during development, and without the complexity of using a dedicated search server?
* Do you want fast Butina clustering? Or MaxMin or sphere exclusion diversity selection?
* Do you work with fingerprints from multiple chemistry toolkits, or have custom fingerprint types?
* Do you want command-line tools with sub-second similarity search times?
* Do you program in Python and want to write new fingerprint analysis programs?
* Do you want the option to have the source code with no time-based licensing?
🔗 https://chemfp.com/
Chemfp - Fast cheminformatics fingerprint search, anywhere you use Python
📄 Chemfp is an analytics platform for cheminformatics fingerprints. It contains command-line tools and an extensive Python library for fingerprint generation, high-performance similarity search, diversity selection, and exploratory research.
# Why chemfp?
* Do you want single-threaded search of 1M 1024-bit fingerprints in under 10 milliseconds?
* Do you want to make a sparse similarity matrix from 1M 2048-bit fingerprints in less than 30 minutes on a four core machine?
* Do you want to include fingerprint similarity results in your Python web application?
... with fast reload times during development, and without the complexity of using a dedicated search server?
* Do you want fast Butina clustering? Or MaxMin or sphere exclusion diversity selection?
* Do you work with fingerprints from multiple chemistry toolkits, or have custom fingerprint types?
* Do you want command-line tools with sub-second similarity search times?
* Do you program in Python and want to write new fingerprint analysis programs?
* Do you want the option to have the source code with no time-based licensing?
🔗 https://chemfp.com/
Quantum Chemistry Package 2023 for Maple Released
The team at RDMChem hopes that you are doing well. Today we are excited to announce the launch of the 2023 Edition of the Quantum Chemistry Package for Maple 2023! The Maple Quantum Chemistry Package 2023 provides a powerful, parallel platform for quantum chemistry calculations that directly integrates as an add-on package into the Maple 2023 environment. It is optimized for both research and education. The Add-on Package (also known as Toolbox) includes density functional theory and wave function methods as well as advanced two-electron reduced density matrix (2-RDM) theories. It is available on Windows, MacOS, and Linux.
The 2023 Package has significant new features and enhancements including:
* New Subpackage for Quantum Computing
* Literature Search via 40+ Million Articles
* Fly-through Molecule Animations
* Custom Hamiltonians in Variational 2-RDM
* Geometries from SMILES Formulas
* Enhanced Editing of Molecular Plots
* Explore Enhancements throughout the Package
https://www.rdmchem.com/
The team at RDMChem hopes that you are doing well. Today we are excited to announce the launch of the 2023 Edition of the Quantum Chemistry Package for Maple 2023! The Maple Quantum Chemistry Package 2023 provides a powerful, parallel platform for quantum chemistry calculations that directly integrates as an add-on package into the Maple 2023 environment. It is optimized for both research and education. The Add-on Package (also known as Toolbox) includes density functional theory and wave function methods as well as advanced two-electron reduced density matrix (2-RDM) theories. It is available on Windows, MacOS, and Linux.
The 2023 Package has significant new features and enhancements including:
* New Subpackage for Quantum Computing
* Literature Search via 40+ Million Articles
* Fly-through Molecule Animations
* Custom Hamiltonians in Variational 2-RDM
* Geometries from SMILES Formulas
* Enhanced Editing of Molecular Plots
* Explore Enhancements throughout the Package
https://www.rdmchem.com/
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The Potential of Artificial Intelligence in Molecular Dynamics
https://ts2.space/en/the-potential-of-artificial-intelligence-in-molecular-dynamics/
https://ts2.space/en/the-potential-of-artificial-intelligence-in-molecular-dynamics/
TS2 SPACE
The Potential of Artificial Intelligence in Molecular Dynamics
The Potential of Artificial Intelligence in Molecular Dynamics TS2 SPACE