Literature DB >> 29096518

The truncated conjugate gradient (TCG), a non-iterative/fixed-cost strategy for computing polarization in molecular dynamics: Fast evaluation of analytical forces.

Félix Aviat1, Louis Lagardère1, Jean-Philip Piquemal1.   

Abstract

In a recent paper [F. Aviat et al., J. Chem. Theory Comput. 13, 180-190 (2017)], we proposed the Truncated Conjugate Gradient (TCG) approach to compute the polarization energy and forces in polarizable molecular simulations. The method consists in truncating the conjugate gradient algorithm at a fixed predetermined order leading to a fixed computational cost and can thus be considered "non-iterative." This gives the possibility to derive analytical forces avoiding the usual energy conservation (i.e., drifts) issues occurring with iterative approaches. A key point concerns the evaluation of the analytical gradients, which is more complex than that with a usual solver. In this paper, after reviewing the present state of the art of polarization solvers, we detail a viable strategy for the efficient implementation of the TCG calculation. The complete cost of the approach is then measured as it is tested using a multi-time step scheme and compared to timings using usual iterative approaches. We show that the TCG methods are more efficient than traditional techniques, making it a method of choice for future long molecular dynamics simulations using polarizable force fields where energy conservation matters. We detail the various steps required for the implementation of the complete method by software developers.

Entities:  

Year:  2017        PMID: 29096518     DOI: 10.1063/1.4985911

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


  6 in total

1.  Molecular Dynamics Simulations of Ionic Liquids and Electrolytes Using Polarizable Force Fields.

Authors:  Dmitry Bedrov; Jean-Philip Piquemal; Oleg Borodin; Alexander D MacKerell; Benoît Roux; Christian Schröder
Journal:  Chem Rev       Date:  2019-05-29       Impact factor: 60.622

2.  Tinker 8: Software Tools for Molecular Design.

Authors:  Joshua A Rackers; Zhi Wang; Chao Lu; Marie L Laury; Louis Lagardère; Michael J Schnieders; Jean-Philip Piquemal; Pengyu Ren; Jay W Ponder
Journal:  J Chem Theory Comput       Date:  2018-09-19       Impact factor: 6.006

3.  Evaluation of molecular photophysical and photochemical properties using linear response time-dependent density functional theory with classical embedding: Successes and challenges.

Authors:  WanZhen Liang; Zheng Pei; Yuezhi Mao; Yihan Shao
Journal:  J Chem Phys       Date:  2022-06-07       Impact factor: 4.304

4.  New scaling relations to compute atom-in-material polarizabilities and dispersion coefficients: part 2. Linear-scaling computational algorithms and parallelization.

Authors:  Thomas A Manz; Taoyi Chen
Journal:  RSC Adv       Date:  2019-10-17       Impact factor: 4.036

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.  Accurate Biomolecular Simulations Account for Electronic Polarization.

Authors:  Josef Melcr; Jean-Philip Piquemal
Journal:  Front Mol Biosci       Date:  2019-12-04
  6 in total

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