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