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Update README.md
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Jedd Bellamy-Carter committed Sep 26, 2020
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Expand Up @@ -5,7 +5,8 @@ A set of scripts for performing consistent gas-phase MD simulations of protein s
## Usage

Perform **`chargePlacer`** calculations on an initial PDB file (`protein_init.pdb`) and generate the corresponding `proton_sites.txt` file for a given charge state. Copy the contents of this folder into the same directory as `protein_init.pdb` and `proton_sites.txt`. Then run:
```bash ./gmx_command_list.sh
```
bash ./gmx_command_list.sh
```

This will iterate through the following steps automatically:
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