Tutorial - Advanced mechanical pulling

This goes beyond what was presented in PLUMED Masterclass 22.15, and which is now available as a Tutorial on this page

This tutorial provides theoretical background then gives a set of exercises for you to complete. You may want to watch the videos that accompany the previous tutorial first.

The flow chart shown below indicates the order in which you should consult the resources. You can click on the nodes to access the various resources. Follow the thick black lines for the best results. The resources that are connected by dashed lines are supplmentary resources that you may find useful when completing the exercise.

Some relevant perspective articles to consider are this one from Hocky and this one from Stirnemann.

Solutions are available from This page

flowchart TB;
  A[FISST tutorial] -.-> B[instructions];
  B -.-> C[Hocky mechanobiology review];
  B -.-> D[Stirnemann mechanobiology review];
  B -.-> E[Computing force dependent rates];
  click A "../../../22/015/data/NAVIGATION.html" "A previous tutorial that introduces the concepts of mechanical pulling in PLUMED and the FISST module"
  click B "INSTRUCTIONS.html" "Instructions for the exercises that you are supposed to complete"
  click C "https://doi.org/10.1021/acs.jpcb.1c06330" "One paper describing how to treat forces in molecular dynamics simulations of biological macromolecules"
  click D "https://doi.org/10.1021/acs.jpcb.1c10715" "A second paper describing how to treat forces in molecular dynamics simulations of biological macromolecules"
  click E "https://doi.org/10.1063/5.0081078" "A paper showing that force-dependent rates can be computed using infrequent metadynamics"