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Homemade scripts based on protocolGromacs, for automatically md system building.

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AutoMdBuilder

Homemade scripts based on protocolGromacs, for automatic md system building.

1. Installation

Please visit following links for more information about installation.

2. Directory Structure

directory_structure

3. Usage

The working directory is 'projects/'. The script 'runme.sh' will first check PDB files in 'projects/structures', then create new directories under 'projects/projects' for each structure, and perform MD system building, minimization, NVT equilibration, NPT equilibration, and so on, as set up in 'scripts/protocolgromacs_001'.

  1. Refine PDB files and copy them to 'projects/structures'.
  2. Update parameters for GROMACS in 'scripts/protocolgromacs_001':
    • 'scripts/protocolgromacs_001/runGromacs.sh'
    • 'scripts/protocolgromacs_001/mdp/*.mdp'
  3. Change the directory to 'projects/'.
  4. Run the script 'runme.sh'.

4. TODO

  • update supporting for multiple ligands
  • update logging

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