Data · dataset · 2019
Free-Energy Surface Prediction by Flying Gaussian Method: Numerical Proof
Listed in Materials Cloud Archive
Biomolecular simulations have a great potential in protein engineering, drug discovery and many other fields.
Description
Unfortunately, this method is computationally expensive, so many interesting processes cannot be routinely studied. In order to address this problem we developed Flying Gaussian method [Journal of Chemical Theory and Computation 12, 4644-4650 (2016)].
This method simultaneously simulates multiple replicas of the studied system and disfavor replicas with similar structures by artificial bias potential. The question arises how to calculate an unbiased free energy surface from a biased simulation. This dataset demonstrates together with mathematical arguments supports application of Umbrella Sampling reweighing method, despite the fact that this method is designed for methods with a time-independent bias potential.
Links
Where it is published
- Materials Cloud Archive record archive.materialscloud.org/records/x0a6z-ptr41 ↗
landing page · from archive materialscloud org
- DOI doi.org/10.24435/materialscloud:2019.0013/v1 ↗
DOI / persistent id · from archive materialscloud org
Catalogue records · 1
- InvenioRDM API archive.materialscloud.org/api/records/x0a6z-ptr41 ↗
metadata API · from archive materialscloud org
Topics
- Stated by source
- flying Gaussian method · metadynamics · molecular dynamics simulation · sampling
- From keywords
- Life Sciences
- Inferred from text
- Biochemistry and cell biology 71% · Simulation 75%
Provenance · 1 source records, 13 field assertions
| Source | Key | Last seen | Raw |
|---|---|---|---|
| Materials Cloud Archive | x0a6z-ptr41 | 2 d ago | JSON v1 |
| Field | Assertion | Extractor | Evidence |
|---|---|---|---|
| access_level | source · archive materialscloud org | connector:archive_materialscloud_org@1.0.0 | |
| concepts[field].anzsrc:group:3101 | enrichment · archive materialscloud org | taxonomy-embedding@1.1.0 | title+keywords+description (71%) |
| concepts[field].local:field:life-sciences | mapping · archive materialscloud org | connector:archive_materialscloud_org@1.0.0 | |
| concepts[method].local:method:simulation | enrichment · archive materialscloud org | keyword-concept-rules@1.0.0 | title+description (75%) |
| concepts[topic].invenio_subject:archive_materialscloud_org:flying-gaussian-method | source · archive materialscloud org | connector:archive_materialscloud_org@1.0.0 | |
| concepts[topic].invenio_subject:archive_materialscloud_org:metadynamics | source · archive materialscloud org | connector:archive_materialscloud_org@1.0.0 | |
| concepts[topic].invenio_subject:archive_materialscloud_org:molecular-dynamics-simulation | source · archive materialscloud org | connector:archive_materialscloud_org@1.0.0 | |
| concepts[topic].invenio_subject:archive_materialscloud_org:sampling | source · archive materialscloud org | connector:archive_materialscloud_org@1.0.0 | |
| description | source · archive materialscloud org | connector:archive_materialscloud_org@1.0.0 | /metadata/description |
| license | source · archive materialscloud org | connector:archive_materialscloud_org@1.0.0 | |
| publication_date | source · archive materialscloud org | connector:archive_materialscloud_org@1.0.0 | |
| title | source · archive materialscloud org | connector:archive_materialscloud_org@1.0.0 | /metadata/title |
| updated_date | source · archive materialscloud org | connector:archive_materialscloud_org@1.0.0 |