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Kitaolab · Feb 27, 2024 · 3d32930 · 3d32930
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diff --git a/docs/src/mdrun/analyzer/ee.md b/docs/src/mdrun/analyzer/ee.md
@@ -3,7 +3,7 @@
 - Snapshots of each cycle are projected onto a 4-dimensional principal component spaces (PCs). Its convex hull is computed and the initial structure of the next cycle is selected from the polygon's vertices.
 - Usage Example
   - Sampling a wide range of phase space without knowing the reference structure
-- See [here](inputfile.md#edgeexpansion) for an example input file.
+- See [here](../inputfile.md#edgeexpansion) for an example input file.
 
 #### keywords
 - **type: str, required**

diff --git a/docs/src/mdrun/inputfile.md b/docs/src/mdrun/inputfile.md
@@ -4,22 +4,21 @@
 - input file must be in [toml format](https://toml.io/en/).
 
 *Contents*
-- [Input file](#input-file)
-  - [sample input file](#sample-input-file)
-  - [basic option](#basic-option)
-  - [simulator option](#simulator-option)
-    - [Gromacs](#gromacs)
-    - [Amber](#amber)
-    - [NAMD](#namd)
-  - [analyzer option](#analyzer-option)
-    - [Target](#target)
-    - [RMSD](#rmsd)
-    - [Association](#association)
-    - [Dissociation](#dissociation)
-    - [EdgeExpansion](#edgeexpansion)
-    - [A\_D](#a_d)
-    - [Template](#template)
-  - [hidden option (No need to specify)](#hidden-option-no-need-to-specify)
+- [sample input file](#sample-input-file)
+- [basic option](#basic-option)
+- [simulator option](#simulator-option)
+  - [Gromacs](#gromacs)
+  - [Amber](#amber)
+  - [NAMD](#namd)
+- [analyzer option](#analyzer-option)
+  - [Target](#target)
+  - [RMSD](#rmsd)
+  - [Association](#association)
+  - [Dissociation](#dissociation)
+  - [EdgeExpansion](#edgeexpansion)
+  - [A\_D](#a_d)
+  - [Template](#template)
+- [hidden option (No need to specify)](#hidden-option-no-need-to-specify)
 
 ## sample input file
 - please check [here](https://github.com/Kitaolab/PaCS-Toolkit/tree/main/jobscripts)
@@ -512,7 +511,7 @@ bound_threshold = 3             # threshold for association to dissociation
   - Number of frames to skip when ranking CVs
 - **threshold: float, required**
   - CV threshold for determining to terminate a trial
-> Template type is a type that can be defined by the user. It is possible to include user-specific variables in input.toml, and these variables can be used in template type in which they are defined. For more information, click [here](reference/template.md).
+> Template type is a type that can be defined by the user. It is possible to include user-specific variables in input.toml, and these variables can be used in template type in which they are defined. For more information, click [here](./analyzer/template.md).
 
 </details>
 

diff --git a/docs/src/mdrun/overview.md b/docs/src/mdrun/overview.md
@@ -69,7 +69,6 @@ loop 0, max_cycle
 end
 ```
 
-- Below is an overview of each component. If necessary, see [Reference](reference.md) for more information on each component.
 - simulator
   - The simulator performs one short MD on the starting structure in cycle 0.
   - In the other cycles, it executes n_replica short MDs, starting from the top-ranking structure of each cycle.

diff --git a/docs/src/quickstart.md b/docs/src/quickstart.md
@@ -44,7 +44,7 @@ pip install -e ".[mdtraj]"
 ## Step3: Preparing input file for PaCS-MD
 - PaCS-MD requires **a toml format input file.** Please make input.toml
   - Please adjust the above settings as needed.
-  - For more information about this file, please refer to [input file](reference/inputfile.md).
+  - For more information about this file, please refer to [input file](./mdrun/inputfile.md).
 ```shell
 vim input.toml
 ```