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PhD Tools

A number of tools and scripts that were initially made for my PhD work.

SAPS - Simulation Analysis and Preparation Suite

Simulation Analysis and Preparation Suite for molecular dynamics and metadynamics. NOW MOVED TO IT'S OWN REPO: MD-SAPS

Python Scripts

  • metaMon: Monitor and analyse remote metadynamics simulations.
  • histidineSeq: Make Hydrophilic Block .pdb structure files from sequence.
  • arrangePdbs: Construct a "brush" of peptides from an input pdb.
  • runReweight: Perform re-weighting on UCB metadynamics data.

PyMOL Scripts

  • Funnel drawing for various projects.
  • Building sequences -> see brush building and beta-sheet maker.
  • Center of Mass (external)
  • PyMOL tips

Simulation Files

  • HPC Benchmarking: Scripts and files for benchmarking high performance computing clusters.
  • Forcefields: Ports of Amber forcefields for use with Gromacs.
  • Submission Scripts: Standard submission scripts for HPC clusters, and for local system preparation.

Bash Scripts