ddx 0.6.0
Libary for domain-decomposition methods for polarizable continuum models
ddX-References

The relevant literature for the ddCOSMO, ddPCM and ddLPB method is listed below. If you're using one of the methods through the ddX-library, please cite the corresponding paper(s).


ddCOSMO:

[1] E. Cancès, Y. Maday, B. Stamm, Domain decomposition for implicit solvation models, Journal of Chemical Physics, Vol. 139, No. 5, pp. 054111 (2013)

[2] F. Lipparini, B. Stamm, E. Cancès, Y. Maday, B. Mennucci, A Fast Domain Decomposition Algorithm for Continuum Solvation Models: Energy and First Derivatives, J. Chem. Theory Comput., Vol. 9, No. 8, pp. 3637–3648 (2013)

[3] F. Lipparini, L. Lagardère, G. Scalmani, B. Stamm, E. Cancès, Y. Maday, J.-P. Piquemal, M. J. Frisch, B. Mennucci, Quantum calculations in solution for large to very large molecules: a new linear scaling QM/continuum approach, J. Phys. Chem. Lett., Vol. 5, No. 4, pp. 953-958 (2014)

[4] F. Lipparini, G. Scalmani, L. Lagardère, B. Stamm, E. Cancès, Y. Maday, J.-P. Piquemal, M. Frisch and B. Mennucci, Quantum, Classical and Hybrid QM/MM Calculations in Solution: General Implementation of the ddCOSMO Linear Scaling Strategy, Journal of Chemical Physics., Vol. 141, pp. 184108 (2014)

[5] S. Caprasecca, S. Jurinovich, L. Lagardère, B. Stamm, F. Lipparini, Achieving linear scaling in computational cost for a fully polarizable MM/Continuum embedding, J. Chem. Theory Comput., Vol. 11, No. 2, pp. 694-704 (2015)

[6] F. Lipparini, L. Lagardère, Ch. Raynaud, B. Stamm, E. Cancès, B. Mennucci, M. Schnieders, P. Ren,Y. Maday, J.-P. Piquemal, Polarizable Molecular Dynamics in a Polarizable Continuum Solvent, J. Chem. Theory Comput., Vol. 11, No. 2, pp. 623-634 (2015)

[7] B. Stamm, L. Lagardère, G. Scalmani, P. Gatto, E. Cances, J. Piquemal, Y. Maday, B. Mennucci, F. Lipparini, How to make continuum solvation incredibly fast in a few simple steps: a practical guide to the domain decomposition paradigm for the Conductor-like Screening Model, Int. J. Quantum Chem. (2019)

[8] M. Nottoli, A. Mikhalev, B. Stamm, F. Lipparini, Coarse-Graining ddCOSMO through an Interface between Tinker and the ddX Library, J. Phys. Chem. B, Vol. 157, (2022)

[9] M. Nottoli, R. Nifosì, B. Mennucci, F. Lipparini, Energy, Structures, and Response Properties with a Fully Coupled QM/AMOEBA/ddCOSMO Implementation, J. Chem. Theory Comput., Vol. 17, No. 9, pp. 5661–5672 (2021)


ddPCM:

[10] B. Stamm, E. Cancès, F. Lipparini, Y. Maday, A new discretization for the Polarizable Continuum Model within the domain decomposition paradigm, J. Chem. Physics, Vol. 144, 054101 (2016)

[11] P. Gatto, F. Lipparini, and B. Stamm, Computation of Forces arising from the Polarizable Continuum Model within the Domain-Decomposition Paradigm, J. Chem. Physics, Vol. 147, 224108 (2017)

[12] M. Nottoli, B. Stamm, G. Scalmani, F. Lipparini, Quantum calculations in solution of energies, structures and properties with a domain decomposition polarizable continuum model, J. Chem. Theory Comput., Vol. 15, No. 11, pp. 6061–6073 (2019)

[13] A. Mikhalev, M. Nottoli, B. Stamm, Linearly scaling computation of ddPCM solvation energy and forces using the fast multipole method, J. Chem. Physics, Vol. 157, 114103 (2022)


ddLPB:

[14] Ch. Quan, B. Stamm, Y. Maday, A Domain Decomposition Method for the Poisson-Boltzmann Solvation Models, SIAM J. Sci. Comput., Vol. 41, No. 2, pp. B320-B350, (2019)

[15] A. Jha, M. Nottoli, A. Mikhalev, Ch. Quan, B. Stamm, Linear scaling computation of forces for the domain-decomposition linear Poisson–Boltzmann method, J. Chem. Physics, Vol. 158, 104105 (2023)