Literature DB >> 27421393

A simple and accurate algorithm for path integral molecular dynamics with the Langevin thermostat.

Jian Liu1, Dezhang Li1, Xinzijian Liu1.   

Abstract

We introduce a novel simple algorithm for thermostatting path integral molecular dynamics (PIMD) with the Langevin equation. The staging transformation of path integral beads is employed for demonstration. The optimum friction coefficients for the staging modes in the free particle limit are used for all systems. In comparison to the path integral Langevin equation thermostat, the new algorithm exploits a different order of splitting for the phase space propagator associated to the Langevin equation. While the error analysis is made for both algorithms, they are also employed in the PIMD simulations of three realistic systems (the H2O molecule, liquid para-hydrogen, and liquid water) for comparison. It is shown that the new thermostat increases the time interval of PIMD by a factor of 4-6 or more for achieving the same accuracy. In addition, the supplementary material shows the error analysis made for the algorithms when the normal-mode transformation of path integral beads is used.

Entities:  

Year:  2016        PMID: 27421393     DOI: 10.1063/1.4954990

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


  7 in total

1.  Prediction of lipid nanoparticles for mRNA vaccines by the machine learning algorithm.

Authors:  Wei Wang; Shuo Feng; Zhuyifan Ye; Hanlu Gao; Jinzhong Lin; Defang Ouyang
Journal:  Acta Pharm Sin B       Date:  2021-12-02       Impact factor: 14.903

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

Authors:  Yuanfei Xue; Jia-Ning Wang; Wenxin Hu; Jun Zheng; Yongle Li; Xiaoliang Pan; Yan Mo; Yihan Shao; Lu Wang; Ye Mei
Journal:  J Phys Chem A       Date:  2021-12-12       Impact factor: 2.944

3.  A generalized class of strongly stable and dimension-free T-RPMD integrators.

Authors:  Jorge L Rosa-Raíces; Jiace Sun; Nawaf Bou-Rabee; Thomas F Miller
Journal:  J Chem Phys       Date:  2021-01-14       Impact factor: 3.488

4.  Theoretical Study on Zearalenol Compounds Binding with Wild Type Zearalenone Hydrolase and V153H Mutant.

Authors:  Ye Liu; Youzhong Wan; Jingxuan Zhu; Zhengfei Yu; Xiaopian Tian; Jiarui Han; Zuoming Zhang; Weiwei Han
Journal:  Int J Mol Sci       Date:  2018-09-18       Impact factor: 5.923

5.  Computational Investigation of Bending Properties of RNA AUUCU, CCUG, CAG, and CUG Repeat Expansions Associated With Neuromuscular Disorders.

Authors:  Amirhossein Taghavi; Ilyas Yildirim
Journal:  Front Mol Biosci       Date:  2022-04-11

6.  Automatized protocol and interface to simulate QM/MM time-resolved transient absorption at TD-DFT level with COBRAMM.

Authors:  Davide Avagliano; Matteo Bonfanti; Artur Nenov; Marco Garavelli
Journal:  J Comput Chem       Date:  2022-07-11       Impact factor: 3.672

7.  Nuclear Quantum Effects from the Analysis of Smoothed Trajectories: Pilot Study for Water.

Authors:  Dénes Berta; Dávid Ferenc; Imre Bakó; Ádám Madarász
Journal:  J Chem Theory Comput       Date:  2020-04-29       Impact factor: 6.006

  7 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.