Literature DB >> 34894680

Affordable Ab Initio Path Integral for Thermodynamic Properties via Molecular Dynamics Simulations Using Semiempirical Reference Potential.

Yuanfei Xue1, Jia-Ning Wang1, Wenxin Hu2, Jun Zheng2, Yongle Li3, Xiaoliang Pan4, Yan Mo1,5,6, Yihan Shao4, Lu Wang7, Ye Mei1,5,6.   

Abstract

Path integral molecular dynamics (PIMD) is becoming a routinely applied method for incorporating the nuclear quantum effect in computer simulations. However, direct PIMD simulations at an ab initio level of theory are formidably expensive. Using the protonated 1,8-bis(dimethylamino)naphthalene molecule as an example, we show in this work that the computational expense for the intramolecular proton transfer between the two nitrogen atoms can be remarkably reduced by implementing the idea of reference-potential methods. The simulation time can be easily extended to a scale of nanoseconds while maintaining the accuracy on an ab initio level of theory for thermodynamic properties. In addition, postprocessing can be carried out in parallel on massive computer nodes. A 545-fold reduction in the total CPU time can be achieved in this way as compared to a direct PIMD simulation at the same ab initio level of theory.

Entities:  

Year:  2021        PMID: 34894680      PMCID: PMC9108008          DOI: 10.1021/acs.jpca.1c07727

Source DB:  PubMed          Journal:  J Phys Chem A        ISSN: 1089-5639            Impact factor:   2.944


  66 in total

1.  Reaction Path Force Matching: A New Strategy of Fitting Specific Reaction Parameters for Semiempirical Methods in Combined QM/MM Simulations.

Authors:  Yan Zhou; Jingzhi Pu
Journal:  J Chem Theory Comput       Date:  2014-06-06       Impact factor: 6.006

2.  Use of the Weighted Histogram Analysis Method for the Analysis of Simulated and Parallel Tempering Simulations.

Authors:  John D Chodera; William C Swope; Jed W Pitera; Chaok Seok; Ken A Dill
Journal:  J Chem Theory Comput       Date:  2007-01       Impact factor: 6.006

3.  Statistically optimal analysis of samples from multiple equilibrium states.

Authors:  Michael R Shirts; John D Chodera
Journal:  J Chem Phys       Date:  2008-09-28       Impact factor: 3.488

Review 4.  QM/MM methods for biomolecular systems.

Authors:  Hans Martin Senn; Walter Thiel
Journal:  Angew Chem Int Ed Engl       Date:  2009       Impact factor: 15.336

5.  Non-Boltzmann sampling and Bennett's acceptance ratio method: how to profit from bending the rules.

Authors:  Gerhard König; Stefan Boresch
Journal:  J Comput Chem       Date:  2010-11-04       Impact factor: 3.376

6.  Comparison of Methods To Reweight from Classical Molecular Simulations to QM/MM Potentials.

Authors:  Eric C Dybeck; Gerhard König; Bernard R Brooks; Michael R Shirts
Journal:  J Chem Theory Comput       Date:  2016-03-23       Impact factor: 6.006

7.  Quantum ring-polymer contraction method: Including nuclear quantum effects at no additional computational cost in comparison to ab initio molecular dynamics.

Authors:  Christopher John; Thomas Spura; Scott Habershon; Thomas D Kühne
Journal:  Phys Rev E       Date:  2016-04-07       Impact factor: 2.529

8.  Multiscale Quantum Mechanics/Molecular Mechanics Simulations with Neural Networks.

Authors:  Lin Shen; Jingheng Wu; Weitao Yang
Journal:  J Chem Theory Comput       Date:  2016-09-06       Impact factor: 6.006

9.  Machine Learning in QM/MM Molecular Dynamics Simulations of Condensed-Phase Systems.

Authors:  Lennard Böselt; Moritz Thürlemann; Sereina Riniker
Journal:  J Chem Theory Comput       Date:  2021-04-05       Impact factor: 6.006

Review 10.  Recent advances in QM/MM free energy calculations using reference potentials.

Authors:  Fernanda Duarte; Beat A Amrein; David Blaha-Nelson; Shina C L Kamerlin
Journal:  Biochim Biophys Acta       Date:  2014-07-16
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  1 in total

1.  Combined QM/MM, Machine Learning Path Integral Approach to Compute Free Energy Profiles and Kinetic Isotope Effects in RNA Cleavage Reactions.

Authors:  Timothy J Giese; Jinzhe Zeng; Şölen Ekesan; Darrin M York
Journal:  J Chem Theory Comput       Date:  2022-06-16       Impact factor: 6.578

  1 in total

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