Lab Stuff
- General Instructions (todo) link
- How to use the computing cluster link + script
See also School wiki (for first time users!) - LAMMPS intro:
Installation
Tutorial0-nve LJ fluids NVE
Tutorial0-nvt LJ fluids NVT
Tutorial1 Polymers
Tutorial2 Knots
Tutorial3 Topo2+Knots
Tutorial3a Topo2+Links
Tutorial4 Dynamic Topo2 w external c++ code
Example Switching protein types with external c++ code
Tutorial5 Reconnections w custom lammps module
Tutorial6 Polymer Recolouring w custom Lammps module
Tutorial7 Ligating polymers of different lengths
Slides from EUTOPIA TRAINING
Recording Part I
Recording Part II
- How to keep a lab book (todo) link
- Intro to Knot Theory (work in progress) link
- Intro to Polymer Physics (work in progress) link
- Tips for presentations and reports (todo) link
- Tips for proposals (todo) link
- Stocks and Materials (todo) link
- Codes: Living polymers: Code to mimic relaxation of (non-equilibrium) living polymers in 1D (from Michieletto, Entropy 2020)
Supercoiled plasmids: Code to model DNA plasmids as twistable chains in LAMMPS. Needs rigid and molecular packages installed (from Smrek et al, Science Advances 2021)
SuperStructure: Parameter-free algorithm to quantify clustered structures in SMLM (STORM) datasets (from Marenda et al, Journal of Cell Biology, 2021)
Topoisomerase on LAMMPS: A LAMMPS fix to simulate a moving Topoisomerase (from Michieletto et al, NAR 2021)
AFM-steered MD simulations of kDNA: Bash and LAMMPS scripts to convert AFM images into a tool to guide MD simulations of corssable DNA rings. (From He et al Phys. Rev. X 2023)
GitLab: For a complete collection of our codes see this GitLab repo