A number of tools and scripts that were initially made for my PhD work.
Simulation Analysis and Preparation Suite for molecular dynamics and metadynamics. NOW MOVED TO IT'S OWN REPO: MD-SAPS
- 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.
- Funnel drawing for various projects.
- Building sequences -> see brush building and beta-sheet maker.
- Center of Mass (external)
- PyMOL tips
- 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.