Package: metadynminer3d 0.0.2
metadynminer3d: Tools to Read, Analyze and Visualize Metadynamics 3D HILLS Files from 'Plumed'
Metadynamics is a state of the art biomolecular simulation technique. 'Plumed' Tribello, G.A. et al. (2014) <doi:10.1016/j.cpc.2013.09.018> program makes it possible to perform metadynamics using various simulation codes. The results of metadynamics done in 'Plumed' can be analyzed by 'metadynminer'. The package 'metadynminer' reads 1D and 2D metadynamics hills files from 'Plumed' package. As an addendum, 'metadynaminer3d' is used to visualize 3D hills. It uses a fast algorithm by Hosek, P. and Spiwok, V. (2016) <doi:10.1016/j.cpc.2015.08.037> to calculate a free energy surface from hills. Minima can be located and plotted on the free energy surface. Free energy surfaces and minima can be plotted to produce publication quality images.
Authors:
metadynminer3d_0.0.2.tar.gz
metadynminer3d_0.0.2.zip(r-4.5)metadynminer3d_0.0.2.zip(r-4.4)metadynminer3d_0.0.2.zip(r-4.3)
metadynminer3d_0.0.2.tgz(r-4.4-x86_64)metadynminer3d_0.0.2.tgz(r-4.4-arm64)metadynminer3d_0.0.2.tgz(r-4.3-x86_64)metadynminer3d_0.0.2.tgz(r-4.3-arm64)
metadynminer3d_0.0.2.tar.gz(r-4.5-noble)metadynminer3d_0.0.2.tar.gz(r-4.4-noble)
metadynminer3d_0.0.2.tgz(r-4.4-emscripten)metadynminer3d_0.0.2.tgz(r-4.3-emscripten)
metadynminer3d.pdf |metadynminer3d.html✨
metadynminer3d/json (API)
| # Install 'metadynminer3d' in R: |
| install.packages('metadynminer3d', repos = c('https://spiwokv.r-universe.dev', 'https://cloud.r-project.org')) |
- acealanme3d - Hills from 30 ns metadynamics of AceAlaNme in water with three collective variable
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 3 years agofrom:f99f72b05a. Checks:OK: 9. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 02 2024 |
| R-4.5-win-x86_64 | OK | Nov 02 2024 |
| R-4.5-linux-x86_64 | OK | Nov 02 2024 |
| R-4.4-win-x86_64 | OK | Nov 02 2024 |
| R-4.4-mac-x86_64 | OK | Nov 02 2024 |
| R-4.4-mac-aarch64 | OK | Nov 02 2024 |
| R-4.3-win-x86_64 | OK | Nov 02 2024 |
| R-4.3-mac-x86_64 | OK | Nov 02 2024 |
| R-4.3-mac-aarch64 | OK | Nov 02 2024 |
Exports:read.hills3dread.plumed3d
Dependencies:base64encbslibcachemclidigestevaluatefastmapfontawesomefsgluehighrhtmltoolshtmlwidgetsjquerylibjsonliteknitrlifecyclemagrittrmemoisemetadynminermimemisc3dR6rappdirsRcpprglrlangrmarkdownsasstinytexxfunyaml
