Literature DB >> 25399133

Quantum, classical, and hybrid QM/MM calculations in solution: general implementation of the ddCOSMO linear scaling strategy.

Filippo Lipparini1, Giovanni Scalmani2, Louis Lagardère3, Benjamin Stamm1, Eric Cancès4, Yvon Maday1, Jean-Philip Piquemal5, Michael J Frisch2, Benedetta Mennucci6.   

Abstract

We present the general theory and implementation of the Conductor-like Screening Model according to the recently developed ddCOSMO paradigm. The various quantities needed to apply ddCOSMO at different levels of theory, including quantum mechanical descriptions, are discussed in detail, with a particular focus on how to compute the integrals needed to evaluate the ddCOSMO solvation energy and its derivatives. The overall computational cost of a ddCOSMO computation is then analyzed and decomposed in the various steps: the different relative weights of such contributions are then discussed for both ddCOSMO and the fastest available alternative discretization to the COSMO equations. Finally, the scaling of the cost of the various steps with respect to the size of the solute is analyzed and discussed, showing how ddCOSMO opens significantly new possibilities when cheap or hybrid molecular mechanics/quantum mechanics methods are used to describe the solute.

Year:  2014        PMID: 25399133     DOI: 10.1063/1.4901304

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  6 in total

1.  Polarizable molecular dynamics in a polarizable continuum solvent.

Authors:  Filippo Lipparini; Louis Lagardère; Christophe Raynaud; Benjamin Stamm; Eric Cancès; Benedetta Mennucci; Michael Schnieders; Pengyu Ren; Yvon Maday; Jean-Philip Piquemal
Journal:  J Chem Theory Comput       Date:  2015-02-10       Impact factor: 6.006

2.  On the polarization of ligands by proteins.

Authors:  Soohaeng Yoo Willow; Bing Xie; Jason Lawrence; Robert S Eisenberg; David D L Minh
Journal:  Phys Chem Chem Phys       Date:  2020-06-04       Impact factor: 3.676

3.  Scalable improvement of SPME multipolar electrostatics in anisotropic polarizable molecular mechanics using a general short-range penetration correction up to quadrupoles.

Authors:  Christophe Narth; Louis Lagardère; Étienne Polack; Nohad Gresh; Qiantao Wang; David R Bell; Joshua A Rackers; Jay W Ponder; Pengyu Y Ren; Jean-Philip Piquemal
Journal:  J Comput Chem       Date:  2016-02-15       Impact factor: 3.376

4.  Implicit Solvents for the Polarizable Atomic Multipole AMOEBA Force Field.

Authors:  Rae A Corrigan; Guowei Qi; Andrew C Thiel; Jack R Lynn; Brandon D Walker; Thomas L Casavant; Louis Lagardere; Jean-Philip Piquemal; Jay W Ponder; Pengyu Ren; Michael J Schnieders
Journal:  J Chem Theory Comput       Date:  2021-03-26       Impact factor: 6.006

5.  Tinker-HP: a massively parallel molecular dynamics package for multiscale simulations of large complex systems with advanced point dipole polarizable force fields.

Authors:  Louis Lagardère; Luc-Henri Jolly; Filippo Lipparini; Félix Aviat; Benjamin Stamm; Zhifeng F Jing; Matthew Harger; Hedieh Torabifard; G Andrés Cisneros; Michael J Schnieders; Nohad Gresh; Yvon Maday; Pengyu Y Ren; Jay W Ponder; Jean-Philip Piquemal
Journal:  Chem Sci       Date:  2017-11-27       Impact factor: 9.825

6.  Electrostatics and water occlusion regulate covalently-bound flavin mononucleotide cofactors of Vibrio cholerae respiratory complex NQR.

Authors:  Soohaeng Yoo Willow; Ming Yuan; Oscar Juárez; David D L Minh
Journal:  Proteins       Date:  2021-06-14
  6 in total

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