Actualités en direct des projets (non traduites)

Détails

Hello GPUGRID! You‘ve already noticed that a new app called “ATM” has been deployed with some test runs. We are working on its validation and deployment, so expect more jobs to come on this app soon. Let me briefly explain what this new app is about. The ATM application The new ATM application stands for Alchemical Transfer Method, a methodology Emilio Gallicchio et al. designed for absolute and relative binding affinity predictions. The ATM method allows us to estimate binding affinities for molecules against a specific protein, measuring the strength at which they bind. This methodology falls under the category of alchemical free energy calculation methods, where unphysical intermediate states are used to estimate the free energy of physical processes (such as protein-ligand binding). The benefits of ATM, when compared with other common free energy prediction methods (like the popular FEP), come from its simplicity, as it can be used with any forcefield and does not require a lot of expertise to make it work properly. Measuring experimental binding affinities between candidate molecules and the targeted protein is one of the first steps in drug discovery projects, but synthesizing molecules and performing experiments is expensive. Having the capacity to perform computational binding affinity predictions, particularly during drug lead optimization, is extremely beneficial. We are actively working now on testing and validating the ATM method so that we can start applying it to real drug discovery projects as soon as possible. Additionally, since these methods are usually applied to hundreds of molecules, it benefits a lot from the parallelization capabilities of GPUGRID, so if everything goes as expected, this could potentially send lots of work units. The ATM app is based on Python, similar to the PythonRL application, where we ship it with a specific python environment. Here are the two main references for the ATM method, for both absolute and relative binding affinity predictions: Absolute binding free energy estimation with ATM: https://arxiv.org/pdf/2101.07894.pdf Relative binding free energy estimation with ATM: https://pubs.acs.org/doi/10.1021/acs.jcim.1c01129 For now we are only able to send jobs to Linux machines but we are hoping to have a Windows version soon.

Source

Création : 3 mars 2023

Détails

As all of you already know we are constantly struggling with our problematic storage. The University have bought a new one and they planned the moving procedure. The HPC cluster should be moved this Monday (March, 6th), the other resources will follow.
I will reasonably shut down the server when needed, I will tell you when as soon as I know the date. Meanwhile the work generator will be active just a few hours a day, so very few workunits will be available.
Thank you all for your understanding and patience.

Source

Création : 2 mars 2023

Détails

Hello everyone,

The following are the new runs for N-Body:

de_nbody_02_27_2023_v182_pal5__data__1
de_nbody_02_27_2023_v182_pal5__data__2
de_nbody_02_27_2023_v182_pal5__data__3

These are our first runs of Palomar 5 with data from SDSS DR17.
Please let me know if there are any issues with these new runs.

Thanks,
Kevin

Source

Création : 27 février 2023

Détails

Dear participants,

There is a wonderful new beginning started by the Science Commons Initiative. They launched a web store selling BOINC-related merchandise. SiDock@home is already on board :)

We support this idea and hope it will help more people to know about BOINC and get interested in BOINC projects! It will also contribute to the development of BOINC as 50% of the profits will go to the BOINC Development Fund (100% in special cases). Another 50% of the profit will go to the project as a donation.

With best wishes,
team of SiDock@home

Source

Création : 23 février 2023

Détails

Indian Ocean experiment

This experiment aims to evaluate the importance of the Indian Ocean Dipole (IOD) event of the winter 2019/2020 on the strong and well predicted North Atlantic Oscillation (NAO) of the same winter. The NAO is of large importance to European winter weather as it governs the winds over the North Atlantic which are related to the mild and wet winters of northern Europe. It has been shown that the NAO is in some years influenced by anomalous tropical ocean conditions (like El Nino). We aim to show that the strong positive IOD of 2019/2020 had an influence on the NAO and resulting warm conditions of this winter. We use the large ensemble of the OpenIFS@Home to identify the connections between the tropical Indian Ocean and the North Atlantic region.

Technical information

CPDN app-name: oifs_43r3
Run time: ~8 hrs/task on a modern CPU
Max memory: ~7Gb
Total number of files: 783 files
Model output: 8.5Mb per output step (uncompressed)
Total size of uploaded files: 2.6GB
Checkpoint filesize: ~800Mb (these are periodically created & deleted in the slot dir and not uploaded)

(The total size of the upload is one member zipped.)

Source

Création : 20 février 2023

Détails

Indian Ocean experiment

This experiment aims to evaluate the importance of the Indian Ocean Dipole (IOD) event of the winter 2019/2020 on the strong and well predicted North Atlantic Oscillation (NAO) of the same winter. The NAO is of large importance to European winter weather as it governs the winds over the North Atlantic which are related to the mild and wet winters of northern Europe. It has been shown that the NAO is in some years influenced by anomalous tropical ocean conditions (like El Nino). We aim to show that the strong positive IOD of 2019/2020 had an influence on the NAO and resulting warm conditions of this winter. We use the large ensemble of the OpenIFS@Home to identify the connections between the tropical Indian Ocean and the North Atlantic region.

Technical information

CPDN app-name: oifs_43r3
Run time: ~8 hrs/task on a modern CPU
Max memory: ~7Gb
Total number of files: 783 files
Model output: 8.5Mb per output step (uncompressed)
Total size of uploaded files: 2.6GB
Checkpoint filesize: ~800Mb (these are periodically created & deleted in the slot dir and not uploaded)

(The total size of the upload is one member zipped.)

Source

Création : 20 février 2023