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Released:
Enhanced sampling of molecular simulations
Project description
AdaptivePELE is a Python module to perform enhancing sampling of molecularsimulation built around the Protein Energy Landscape Exploration method (PELE) developed in the Electronic and Atomic Protein Modelling grop (EAPM) at the Barcelona Supercomputing Center (BSC).
Usage
AdaptivePELE is called with a control file as inputparameter. The control file is a json document that contains 4 sections:general parameters, simulation parameters, clustering parameters and spawningparameters. The first block refers to general parameters of the adaptive run,while the other three blocks configure the three steps of an adaptive samplingrun, first run a propagation algorithm (simulation), then cluster thetrajectories obtained (clustering) and finally select the best point to startthe next iteration (spawning).
An example of usage:
Installation
There are two methods to install AdaptivePELE, from repositories, either PyPI or Conda (recommended), or directly from source.
To install from PyPI simply run:
To install from Conda simply run:
To install from source, you need to install and compile cython files in the base folder with:
Also, if AdaptivePELE was not installed in a typical library directory, a common option is to add it to your local PYTHONPATH:
Documentation
The documentation for AdaptivePELE can be found here
Contributors
Cleanmymac x 4 4 3 1557 key free key. Daniel Lecina, Joan Francesc Gilabert, Oriol Gracia, Daniel Soler
Mantainer
Joan Francesc Gilabert (cescgina@gmail.com)
Citation
Fusion 250 scooter. AdaptivePELE is research software. If you make use of AdaptivePELE in scientific publications, please cite it. The BibTeX reference is:
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| Filename, size | File type | Python version | Upload date | Hashes |
|---|---|---|---|---|
| Filename, size AdaptivePELE-1.6.3.tar.gz (7.3 MB) | File type Source | Python version None | Upload date | Hashes |
Hashes for AdaptivePELE-1.6.3.tar.gz
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|---|---|
| SHA256 | 34be232bc04bde2dcc4ebd900dd9c71e6f25eed93b7c875463c07d3dd8ce1aa9 |
| MD5 | 2c83d4cd38e95157526500f0cb08b1cc |
| BLAKE2-256 | 252c65b787dc210294855b8f27abeb4a7761f25fce34e0b8bfd56779c679440d |
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