Dr. Omar Valsson
- Department of Chemistry, University of North Texas
- www.valsson.info
- omar.valsson@unt.edu
- @OmarValsson
The slides can be found here
- PLUMED Homepage
- PLUMED-NEST: Repository of PLUMED Input files
- The official manual for PLUMED version 2.9 can be found here
- Various other PLUMED tutorial can be found in the manual
- PLUMED Masterclass
- Corresponding YouTube videos with lectures and solutions found here
- Masterclass 21.1: PLUMED syntax and analysis
- Masterclass 21.2: Statistical errors in MD
- Masterclass 21.3: Umbrella sampling
- Masterclass 21.4: Metadynamics
- Masterclass 21.5: Simulations with multiple replicas
- Masterclass 21.6: Dimensionality reduction
- Masterclass 21.7: Optimizing PLUMED performances
- Masterclass 22.3: OPES method
- Masterclass 22.11: Variationally enhanced sampling with PLUMED
- https://doi.org/10.33011/livecoms.4.1.1583
- https://doi.org/10.1146/annurev-physchem-040215-112229
- https://doi.org/10.1038/s42254-020-0153-0
- https://doi.org/10.1007/978-3-319-44677-6_49
- https://doi.org/10.1007/978-1-4939-9608-7_21 (also https://arxiv.org/abs/1812.08213)
- https://doi.org/10.1039/d1cp04809k
- https://doi.org/10.1021/acsomega.2c06310
- https://doi.org/10.1103/physreve.107.l012601
- https://doi.org/10.1140/epjb/s10051-021-00233-5
- https://doi.org/10.1021/acs.jctc.0c00355
- https://doi.org/10.1080/00268976.2020.1737742
- https://doi.org/10.1017/qrd.2022.23
- https://doi.org/10.1016/j.sbi.2019.12.016
- https://doi.org/10.48550/arXiv.2303.08486
- Graph of a rational switching function
This tutorial will be run through a Jupyter notebook via OnDemand. Thus, access the OnDemand in the normal way and create a new jupyter notebook instance and load the MetaD-Tutorial.ipynb notebook.
Note: here we will use the normal Python kernel, not the icomse-cpu one