Intramolecular and water mediated tautomerism of solvated glycine. J. Chem. Inf. Model. 2024, 64, 9, 3599–3604. arXiv
From DFT to DeePKS to DeePMD | DeePKS Basics
From DFT to DeePKS to DeePMD | DeePKS Toturials
OPES (on-the-fly probability enhanced sampling)
Voronoi CVs for enhanced sampling autoionization and tautomerism
Note: The above web links have Chinese to English translations.
The dataset for training the DP model is uploaded to AIS Square and Zenodo.
The compressed DP model is uploaded to AIS Square and Zenodo.
Requiring the installation of the OPES module. To use additional Voronoi CVs code, put the three .cpp files above into /your_plumed_path/plumed/src/colvar, and then compile plumed. The Voronoi CV VORONOID2.cpp, VORONOIS1.cpp, VORONOIC0.cpp code files are linked to CVs named s_d, s_p, s_a as illustrated in the paper and SI. Other Voronoi CVs can be used to calculate the diffusion coefficient for H₃O⁺ or OH⁻ ions.
More Voronoi CVs can be utilized for the water autoionization.
Incorporating lammps and plumed, follow plumed-feedstock to overlay default plumed version or use LOAD command.
Incorporating plumed