diff --git a/README.md b/README.md index 2e345dd..04ad230 100644 --- a/README.md +++ b/README.md @@ -1,11 +1,10 @@ # WESTPA Tutorials Landing Page/Hub -This is the landing page/hub for all [WESTPA Tutorials](https://github.com/westpa/westpa/wiki/Tutorials). If you are here to learn how to use WESTPA, you are at the right place! +This is the landing page/hub for all [WESTPA Tutorials](https://github.com/westpa/westpa/wiki/tutorials). If you are here to learn how to use WESTPA, you are at the right place! -If you are new to WESTPA, start off with the original suite of tutorials (for WESTPA 2.0) \([Bogetti et al. 2019](https://livecomsjournal.org/index.php/livecoms/article/view/v1i2e10607)\). The `original_suite` folder contains links to the required files. - -For more advanced users who have completed those tutorials, try out our advanced tutorials (To be published). Necessary files are linked in the `advanced_tutorials` folder. +If you are new to WESTPA, start off our suite of tutorials for WESTPA 2.0 \([Bogetti et al. 2023](https://doi.org/10.33011/livecoms.5.1.1655 )\). [Tutorials 7.1-7.4](https://github.com/westpa/westpa_tutorials) are our basic and intermediate tutorials. [Tutorials 7.5-7.10](https://github.com/westpa/westpa2_tutorials) are our advanced tutorials. +If you decide to clone this repository using `git` in the command line, make sure to use `git clone --recursive https://github.com/westpa/tutorials` so you also clone the tutorial files submodules. If you already cloned the repo without the `--recursive` flag, run `git submodule update --init --recursive` in the root level of the clone to download the submodules. ### Updating this repository diff --git a/old_tutorials/original_suite/WESTPA2 b/old_tutorials/original_suite/WESTPA2 index e9cacaf..12d3be7 160000 --- a/old_tutorials/original_suite/WESTPA2 +++ b/old_tutorials/original_suite/WESTPA2 @@ -1 +1 @@ -Subproject commit e9cacafa0e2b63ec3a8c518a2aac94b1c8f687bb +Subproject commit 12d3be7002766474f9cf97723d5a235ad5b73133 diff --git a/paper/CombinedSuiteofWESTPATutorials.pdf b/paper/CombinedSuiteofWESTPATutorials.pdf index 64e4158..d8b1517 100644 Binary files a/paper/CombinedSuiteofWESTPATutorials.pdf and b/paper/CombinedSuiteofWESTPATutorials.pdf differ diff --git a/paper/TutorialManuscript/03_workflow.tex b/paper/TutorialManuscript/03_workflow.tex index 9bc577c..4141b5d 100644 --- a/paper/TutorialManuscript/03_workflow.tex +++ b/paper/TutorialManuscript/03_workflow.tex @@ -158,7 +158,7 @@ \section{Additional Simulation Workflow with WESTPA 2.0 Upgrades} As discussed in \textbf{Section \ref{tut:binless}}, these "basis" structures will govern the recycling process (if used), so care should be exercised in choosing them. In the third (“Go/Analyze”) stage, we recommend applying one of the following three options to further accelerate convergence to a steady state once successful pathways are generated. -The Rates from Event Durations (RED) analysis scheme \citep{degrave_red_2021} estimates rate constants more efficiently than the original WE scheme \citep{huber_weighted-ensemble_1996} by exploiting information in the transient region of the simulation. +The Rates from Event Durations (RED) analysis scheme \citep{degrave_red_2021} estimates rate constants more efficiently than the original WE scheme \citep{huber_weighted-ensemble_1996} by exploiting information in the transient region of a simulation and can only be used with a non-equilibrium steady-state simulation. Another option is the haMSM plugin, which employs a fine-grained “microbin” analysis and can be used to not only estimate rate constants following WESTPA simulation (e.g., for the seconds-timescale coronavirus spike opening process \citep{casalino_ai-driven_2021}), but to also restart trajectories with their weights adjusted for a steady state \citep{russo_westpa_2022}. Because restarts in the haMSM plugin are initiated from configurations occurring throughout previously run trajectories, the continuity of the generated pathways is broken. The third option is the weighted ensemble steady state (WESS) plugin \citep{bhatt_steady-state_2010}, which uses the less fine-grained WE bins to estimate steady state but preserves the continuity of pathways, restarting from only the final points of trajectories. diff --git a/paper/TutorialManuscript/03a_old_tutorials.tex b/paper/TutorialManuscript/03a_old_tutorials.tex index a5e65a9..fa0e1e9 100644 --- a/paper/TutorialManuscript/03a_old_tutorials.tex +++ b/paper/TutorialManuscript/03a_old_tutorials.tex @@ -598,8 +598,8 @@ \subsubsection{Brute Force Simulations} \end{verbatim} The command-line arguments are the RMSD data file, time interval at which the RMSD values are calculated in seconds, and threshold RMSD values for the folded and unfolded states in Angstroms. -The rate constant of unfolding is estimated to be 0.13 x 108 s\textsuperscript{-1} (confidence interval: 0.09 x 108 s\textsuperscript{-1} – 0.18 x 108 s\textsuperscript{-1}) and that of folding is estimated to be 0.71 x 107 s\textsuperscript{-1} (confidence interval: 0.44 x 107 s\textsuperscript{-1} – 1.24 x 107 s\textsuperscript{-1}). -Confidence intervals are derived from a Bayesian bootstrapping procedure \citep{mostofian_statistical_2019}. +The rate constant of unfolding is estimated to be 0.13 x 108 s\textsuperscript{-1} (credibility region: 0.09 x 108 s\textsuperscript{-1} – 0.18 x 108 s\textsuperscript{-1}) and that of folding is estimated to be 0.71 x 107 s\textsuperscript{-1} (credibility region: 0.44 x 107 s\textsuperscript{-1} – 1.24 x 107 s\textsuperscript{-1}). +Credibility regions are derived from a Bayesian bootstrapping procedure \citep{mostofian_statistical_2019}. \subsubsection{Using WESTPA} diff --git a/paper/TutorialManuscript/04_binless.tex b/paper/TutorialManuscript/04_binless.tex index b24ab3a..7bcddbf 100644 --- a/paper/TutorialManuscript/04_binless.tex +++ b/paper/TutorialManuscript/04_binless.tex @@ -78,7 +78,7 @@ \subsubsection{Setting up the WE Simulation} type: RectilinearBinMapper boundaries: # Under base: - [0, 2.60, 'inf'] - mappers: + mappers: - type: BinlessMapper ngroups: [5] # Number of groups ndims: [1] # Number of grouping diff --git a/paper/TutorialManuscript/05_membrane.tex b/paper/TutorialManuscript/05_membrane.tex index 0c4feed..91c82be 100644 --- a/paper/TutorialManuscript/05_membrane.tex +++ b/paper/TutorialManuscript/05_membrane.tex @@ -91,7 +91,7 @@ \subsubsection{Preparing the simulation} type: RectilinearBinMapper boundaries: - [-inf, -44, 34, inf] - mappers: + mappers: - type: MABBinMapper nbins: [20] # Number of bins direction: [0] # Split both directions diff --git a/paper/TutorialManuscript/07_analysis.tex b/paper/TutorialManuscript/07_analysis.tex index 90a0eed..0af6538 100644 --- a/paper/TutorialManuscript/07_analysis.tex +++ b/paper/TutorialManuscript/07_analysis.tex @@ -201,7 +201,7 @@ \subsubsection{Calculating rate constants using the original WE scheme} Move this file to the \verb|analysis/| folder that was generated by \verb|w_assign| and proceed with the analysis. Note that the above is not part of the following tutorial and is only included to provide an example to users of how to perform an analysis on auxiliary data. -\textbf{2. Correct the Fluxes using the RED Scheme.} To correct the calculated fluxes using the RED scheme, we apply the \verb|w_red| command-line tool, which will read in the \verb|rate_evolution| and durations datasets in your \verb|direct.h5| file and calculates a correction factor for the flux value at each iteration. +\textbf{2. Correct the Fluxes using the RED Scheme.} To correct the calculated fluxes using the RED scheme, we apply the \verb|w_red| command-line tool, which will read in the \verb|rate_evolution| and \verb|durations| datasets in your \verb|direct.h5| file and calculates a correction factor for the flux value at each iteration. The RED scheme should only be applied on WE simulations sampled in non-equilibrium steady-state conditions, where trajectories are recycled at a target state(s). This scheme is not compatible with the WESS and WEED plugins for reweighting trajectories on-the-fly . To use this tool, add the following to the analysis section of your \verb|west.cfg| file: \begin{verbatim} red: diff --git a/tutorials7.1-7.4 b/tutorials7.1-7.4 index 26c4c37..0db92b6 160000 --- a/tutorials7.1-7.4 +++ b/tutorials7.1-7.4 @@ -1 +1 @@ -Subproject commit 26c4c37b4844296faed2a00942db95e0de0aa5ed +Subproject commit 0db92b6a2a0493f120a0b6bc00a0fdba9769bf09 diff --git a/tutorials7.5-7.10 b/tutorials7.5-7.10 index 4d5f5ec..92fa8e7 160000 --- a/tutorials7.5-7.10 +++ b/tutorials7.5-7.10 @@ -1 +1 @@ -Subproject commit 4d5f5ece3937dba70e843e7e69f2c81d9da0b6eb +Subproject commit 92fa8e791980c199733568ef55ba7f2fb421ba84