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README.md

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Folder organization

  1. wt_mdyn: wt stands for "well-tempered". It contains the metadynamics simulations
  2. tpr_generation: It contains the procedure for the generation of the .tpr files for the four cases
  • non-myristoylated Recoverin (nmRec)
  • non-myristoylated Recoverin in complex with GRK1 (nmRec_GRK1)
  • Recoverin in membrane (membr_Rec)
  • Recoverin with GRK1 in membrane (membr_Rec_GRK1) It contains as well 10 ns of unbiased simulations.
  1. explorative_meta: it contains the analysis of metadynamics runs performed with different methodologies reported in the plumed manual (for instance, parallel bias metadynamics, frequency adapted metadynamics and so on).
  2. benchmarks: contains the benchmarks on CPU/GPU of both nmRec and membr_Rec
  3. ideas: contains some possible ideas such as the coarse-grained metadynamics and so on. This folder does not present any type of analysis, it's purely speculative
  4. box_change: the box size is changed in order to let the ion sample the unbound state without interacting with the nearest periodic image of the protein. Essentially, the steps described in tpr_generation are performed again.

funnel_bias_30ns Position of the Calcium ion during biased funnel metadynamics simulation

FE_profile.mp4

smaller_funnel Representation of the funnel restraint

CaM_coordinated Multisite calcium coordinated by the neighboring residues

Observations

I think that the multiple walker is the best protocol as it provides a huge speedup. Moreover, the walkers can be differentiated in terms of height and width of the Gaussians and bias factor as well.

Another protocol, which is explicitly treated in wt_mdyn is the funnel metadynamics.