A First Test Run Using Gyration Radius

It is crucial here to observe the so-called recrossing events, which means that the putative transition state is being explored by metadynamics many times. This ensures that the interesting states are sampled exhaustively, which is 

Frequently, there exist other significant diagnostics that can highlight problems in the CV choice and may help in devising a more suitable CV. For example, using an independent structural comparison consisting of a different descriptor, such as root mean square deviation (RMSD) after optimal 

Time evolution of the radius of gyration (upper panel) along with Root 

Mean Square Deviation (RMSD) after optimal fit onto and reference 

This scenario points to the fact that the selected set of CVs is not suitable and a different choice should be made. 

---

The first example refers to the case where MetaD is performed on gyration radius reported in Section A First Test Run Using Gyration Radius. Note that in PLUMED one can also monitor other variables that might be helpful in checking the results of the simulation (in this case O and T dihedral angles) ... 

---