Getting Started With Nested Binning Scheme

[shelby case]

Hello, 

I am curious if anyone has any resources or tips for implementing nested bins in WESTPA using gromacs? 

I have been using a 1D progress coordinate to sample a transition from one state to another (aiming to get equilibrium dist), but my progress along this coordinate (and many others) has been limited by an orthogonal barrier; see below. 

WE result (using TIC1 featurized by internal coordinates): 

Reference MD data:

I think my run could benefit from nested bins from TIC4 at the start (i.e. TIC1 bin boundaries -1.5,-0.75) and the end (i.e. TIC1 bin boundaries 1,1.5) (also ignore the values of the tic4, I corrected the mean centering after these graphs were made, the same nesting bin concept holds). 

Any help or resources would be greatly appreciated. 

Thank you, 

Shelby Case

[Jeremy Leung]

Hi Shelby,

The format is very similar to that of what you do for MAB (Tutorial 7.6), except when you would use another RectilinearBinMapper instead.

See here (in one of the commented blocks): https://github.com/jeremyleung521/odld/blob/79e2d61e35b6c6b0f254561861c1ed7c9a9226bb/west.cfg

Best,

Jeremy L.

[shelby case]

Thanks Jeremy, 

Is there a specific way I would store pcoord values for two dimensions? Do you have any reference code I can use? 

Thank you, 

Shelby 

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[Jeremy Leung]

Hi Shelby,

Tutorial 7.2 is a classic one to follow:

https://github.com/westpa/westpa_tutorials/tree/main/tutorial7.2-p53

A more modern example (done with newer WESTPA 2 features, since I recall you're on an older WESTPA version):

https://github.com/westpa/westpa-test-systems/tree/main/alanine_dipeptide_plain_80

Best,

Jeremy L.

[shelby case]

Hello, 

I have been trying to implement a 2D progress coordinate but it seems that im not able to initialize my WESTPA run and there is no descriptive error message. Im I missing something in my pcoord.py or west.cfg that could be preventing my run from starting? 

Thank you, 

Shelby 

[Hayden Scheiber]

Hi Shelby,

Your westpa configuration binning is still configured for 1D pcoords. In particular, see my comments below:

bins: type: RecursiveBinMapper base: type: RectilinearBinMapper boundaries: - ["-inf", 2] # This only refers to first pcoord

- [lower, upper] # Need to define an outer boundary for your second pcoord here mappers: - type: MABBinMapper nbins: [100, n_bins_in_pcoord2] # Need to decide on how many bins are created along each dimension at: [-0.5, pcoord2] # Also need to point "at" along all dimensions # end MAB bin_target_counts: 30

cheers,

Hayden