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Merge pull request #174 from brookehus/typo-fix
fix typo
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notebooks/00-pentapeptide-showcase.ipynb

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@@ -243,7 +243,7 @@
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"the first four dimensions contain all relevant information of the slow dynamics.\n",
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"\n",
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"Based on this result, we try a TICA projection with lag time 0.5 ns (5 steps).\n",
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"Please note that this is a modeler's choice based on the best heuristics that is currently available to our knowledge. \n",
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"Please note that this is a modeler's choice based on the best heuristic that is currently available to our knowledge. \n",
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"It might be necessary to re-adjust the TICA lag time after the MSM estimation. \n",
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"\n",
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"\n",
@@ -350,7 +350,7 @@
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"⚠️ It is a priori unclear what the optimal number of cluster centers $k$ is.\n",
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"It largely depends on the distribution of our data and on the number of dimensions we use.\n",
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"\n",
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"In the following, we will estimate unvalidated Markov models using different numbers of cluster centers and use the VAMP-2 score (using cross validation) as a heuristics.\n",
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"In the following, we will estimate unvalidated Markov models using different numbers of cluster centers and use the VAMP-2 score (using cross validation) as a heuristic.\n",
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"This approach requires us to guess the MSM lag time, which we set to the TICA lag time of $5$ steps (or $0.5$ ns).\n",
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"Since the clustering algorithm is stochastic,\n",
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"we conduct multiple rounds of discretization at each number of cluster centers."
@@ -394,7 +394,7 @@
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"We will use this number for further analysis.\n",
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"\n",
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"As already stated above, the score has been generated using MSMs that were not validated,\n",
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"meaning that the above plot is really just a heuristics.\n",
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"meaning that the above plot is really just a heuristic.\n",
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"Besides having an optimal score, we want to obtain a model that describes physically interesting states.\n",
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"Thus, the number of states $k$ is often re-adjusted after model inspection."
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"The highest $k$ can be adjusted using the `mlags` keyword argument of `msm.cktest()`.\n",
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"\n",
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"Since we can only inspect the result for a small number of (macro-) states,\n",
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"we use the implied timescales plot as a heuristics to estimate a number of metastable states to test for. \n",
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"we use the implied timescales plot as a heuristic to estimate a number of metastable states to test for. \n",
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"We can resolve $4$ slow processes up to lag times of $2.5$ ns.\n",
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"Since the Chapman-Kolmogorov test involves estimations at higher lag times,\n",
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"we will attempt to capture those processes choosing $5$ metastable states."

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