RealQM for Protein Folding

RealQM is now implemented with the help of Claude for up to 100 atoms on a 200^3 grid which allows simulation of a beta hairpin peptide as a miniature protein which folds: 

You can test the code on GitHub as molecule.js, moleculedyn.js, hairpin.html, water100.html, and caffeine.html. The code uses one density and support function defined on the 200^3 grid and so runs on a MacBook Air M4 with 50 frames/s.  Upscaling to 1000 atoms on 300^3 grid with 10 frames/sec in pipe line.  

Here is first RealQM run in static mode on the calcium-regulated actin-binding protein Villin:

• HP35-like three-helix bundle: 
• 51 polyalanine residues in 3 alpha helices (antiparallel arrangement) 
• 510 protein atoms (N, H, Ca, Ha, Cb, 3Hb, C, O per residue)
• Hydration shell of ~163 water molecules filling remaining slots to 
• ~999 atoms on 300³ grid, mid slice with white dots out of plane atoms
• 3-line code updates electron densities and free boundary between densities + solves Poisson by multi-grid.

 Next is to run RealQM in dynamic mode to see if folding is captured. Watch out...