home.md

@@ -4,16 +4,16 @@ This wiki provides instructions on general and EUREKA-specific Gromacs methods
 
 ## Contents
 
-*  Input preparation
-   -   [Generating Topologies for an Arbitrary PDB](Generating-Topologies-for-an-Arbitrary-PDB)
-   -   Unit Cells and Solvation
-   -   Neutralisation
-*  Energy Minimisation and Equilibration
-   -   Energy minimisation
-   -   NVT Equilibration
-   -   NPT Equilibration
-*  Molecular Dynamics
-*  Analysis
-   -   Quantifying average motion
-   -   Animating the system
-   -   PLUMED?
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+*  1) Input preparation
+   -   a) [Generating Topologies for an Arbitrary PDB](Generating-Topologies-for-an-Arbitrary-PDB)
+   -   b) Unit Cells and Solvation
+   -   c) Neutralisation
+*  2) Energy Minimisation and Equilibration
+   -   a) Energy minimisation
+   -   b) NVT Equilibration
+   -   c) NPT Equilibration
+*  3) Running the Dynamics
+*  4) Analysis
+   -   a) Quantifying average motion
+   -   b) Animating the system
+   -   c) PLUMED?
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